This is a general compilation of thoughts I had while testing this.

Speed:
Run speed is a no-brainer in such mods, and it is not bad at all, especially in the early game. But why dedicate two separate skills to this? Why make the last one weaker per point invested? And I'm not even talking about the third, combat-oriented one (which is good by itself, but combined with the basic speed perk probably trivialises early combat by a lot).
Repeating skill effects is a recurring problem throughout the mod.
And there's an extra inserter stack bonus here for some reason.

Survival:
The survival part is even "better," having 3 out of 5 perks dedicated to max health (again, for some reason the earlier skills are stronger than the later ones, which maybe I just don't understand).
In my opinion, there is no reason to make repeating skills. Make the tree smaller, make the skill cap bigger, but repeating just feels unrewarding and cheap.

Combat:
Rapid Deployment is almost useless.
It only uses drones from the inventory, and the only real benefit is that those drones don't count as followers. Yes, they also don't follow the player, but at least it can be a bit useful. Deploying a bunch of them isn't helping at all either. Drones aren't used much in general due to their cost and low lifetime, and autodeployment feels like an additional waste of resources. I have a suggestion for a remake of that skill, but that is for another topic.
And THE FOURTH health upgrade???

Production:
Mining productivity again appears as two separate skills, with the first one being significantly weaker than the last one. +115% total mining productivity in the early game is insane, especially combined with furnace and steel productivity. I don't mind significant bonuses, but this is too much for almost no cost at all. I know that all skill mods are supposed to be unbalanced at their core, but this feels absolutely undeserved and should not be achievable so easily.
Yes, I get that the player cannot get everything at once, and while other skills can be chosen to make a strong effect, others will get almost no development to pay the cost. I can't test how long it will take in general to get those results, but I already see that a significant part of all skills can be achieved easily just with the first two–three science packs, even without abusing some XP gain mechanics.
In addition, manual crafting speed (also repeated from the Speed tab) and mining reach are player-character-directed skills; there is no place for them in the Factory tab.

Knowledge:
Again, 3 out of 5 skills are Research speed. Noticing a pattern, huh. IMO, this whole tab needs a complete rework, as none of the 5 skills are meaningful here:
(x - - x x) Research speed by itself is one of the most useless techs you can get. Yes, with all skills it stacks up to x4 from the base speed, but it really makes sense only in late-game megabasing or some extra costly mod setups. Unless something makes it that way, there is almost no additional cost to just double your labs to gain this exact result. I can understand one skill for lab speed, and somewhere in the middle (early it is useless, late-game you want stronger effects for point investments, as they get harder and harder to get), but 3 is too much.
(- - x - -) 80 XP per lab research is pathetic compared to the amount of points you need (thousands and tens of thousands per level after the early game). It is a good idea, but it should not be static. It requires some scaling: the more a tech costs and the more time it takes per unit, the more XP it gives. At least then it will be useful unless you unlock every skill, and it won't make it overpowered early, while tech costs only ~20 packs each.
(- x - - -) Inserter stack bonus. Really.

Logistics (new, shiny):
I can't actually say anything bad about this tab. For now, it feels the most balanced.
Drone Battery capacity is a neat addition, as the only other ways to increase it are quality and other mods. Because of that, it is probably wise to increase the cap from 160% to 200–250%, IDK.
16 trash slots is just… meh. Why would I want to invest in that? I can't say it is completely useless, but it's very niche. Maybe just change it to a round number (20) and revise later.
16 drone cargo slots (why is "16" so recurring here?) is also way over the top. Its usefulness is also a bit niche, but vanilla gives you 4 max capacity, and adding +16 on top is just… wow. It's way too strong, but at the same time gives a very narrow advantage. Maybe this balances it out? I don't know.
Belt Mastery—I could not get it to work, even though it shows in the bonus tab (it caps at the vanilla size of 4 even while the bonus tab shows any bigger number).
Aside from that issue—yes! It is good, it is in its place in the correct tab with the correct order as the last skill. Maybe make it more costly and way more expensive to get after the first level, so it doesn't get too overpowered before Gleba, and still leave the initial research as the main source of that bonus. Like, you can get +1 from the first level if you invest more than usual, and you can get +4 from Gleba. Still want more or completely abandon Space Age tech? Well, you can, but that will cost you way more!

Engineering:
Alternative recipes—love it!
But despite being interesting, it has downsides.
Firstly, I don't understand why 5 / 6 entries here grant crafting speed (and I assume it's just manual crafting speed). The main benefits are the recipes themselves; there is no need to add anything on top. Plus, the recipes are what I want to see as bonus text on the skill, so I don't need to read into the description to know about that.
About recipes—this is strong! And it's a gift and a curse at the same time. Because of how strong they are, but how easily obtainable, there is no real reason to use basic recipes. You can easily get them as soon as you get close to a particular part of the playthrough. But on the other hand, this is the effect I want to see in mid–late game. Make my circuit rivers take 1/3 of the copper? Yes, please! And this is also way more interesting (!!!) than just plain item productivity (which is also capped at +300% anyway). It just needs to be more deserved. Quick solution: make these skills way more costly. Like, 5–10 times more points. Then get rid of the crafting speed bonus and leave each skill as one expensive level.
About Production Mastery—that would be boring if it wasn't containing several parts in itself. I'm usually not a big fan of productivity via research/effect, but this makes it at least more interesting. I would like to see it reworked later, but for now it's decent and not too overpowered with their max 40%.

Capstone skills:
I like that they are locked behind other tech, and even several with different levels. It lacks some visual representation of what skill I need, but I don't know how to do it, aside from some visual hints (like highlighting the correct tab when hovering over the required skill name? IDK how hard that is).
I will not say that "You need more." It's better to make less, but interesting, higher-quality skills than just populate tabs with useless/repeating effects.
The only thing I can say: Synergy should tell what exact bonuses it gives, rather than just "All character stats," and Research productivity should be locked behind Knowledge (and maybe Production/Logistics/Engineering) tabs' skills, and not by Synergy, as they are too different.

Other stuff:

Inserter stack bonus is insane, out of place, and also doesn't affect stack and bulk inserters (didn't try with other mods, but keep in mind that it should work). It makes more sense to place one skill in the Logistics tab (maybe even replace trash slots) with a cap of 1–3 (more just doesn't make a big difference, especially combined with vanilla tech), and maybe one more only for stack and bulk inserters with a bit higher cap to complement their already big hands with full research.

Skill lower text contains extra text of cost when unlocked, but no points invested. Cost is the same info as on the button right next to it, and there is no such text when you invest at least 1 point, which is OK.

The skill menu should be closed with the Esc button, like the inventory, Factory Planner, and various other menus. Just a small QoL feature. It would also be good to make the 'x' button just like on those menus instead of the "Close" button in the opposite corner.

The "Invests per click" amount part is obsolete. I think it's better to:
"LMB = +1"
"RMB = -1" (yes, it is a request for a decrease-level feature)
"Shift + MB = ×5" — depends on LMB or RMB to increase/decrease
"Ctrl + MB = max" — depends on LMB or RMB to increase/decrease

XP gain needs to be reworked. For now, the most effective way to gain it (at least what I found) is handcrafting tons of cheap, fast stuff, and the alt-gear recipe suits that perfectly. Even if handcrafting is a way to gain XP, it should not be a flat number, but scale at least from crafting speed (so crafting 10 items in 0.5 sec and one item in 5 sec will yield the same) and maybe resource cost and progression stage, so later recipes would give way more points than just thousands of gears, and crafting a substation would be preferable to a wooden pole, despite the pole being way cheaper. But even in that scenario, I don't think that manual actions should be the way to go in the long run; it is a game about automation after all.

The skill window name and skill points amount lines have an extra "*" char at the front, which doesn't convey any information, but I'm probably just being too hard on it and should stop.

The Factory and Engineering tabs have inner borders because of the scroll bar, and other tree tabs don't. Not sure you can do something about it, but maybe…

Holy crap, what is that wall of shitpost i just wrote...

Wow, this is the one! Before even reading it all, this is why I uploaded it, in the hopes of getting fresh ideas!

Speed: There are some redundant speed elements in there, I honestly thought I had got through it, but as you can imagine I have reset my skills many times and the max skills button is there for that purpose, I start to not see the wood for the trees. I will take another pass for adjustments.

Engineering: Yes, agreed 100%, there are going to be balancing issues for a while, the alt recipes are powerful. They could perhaps be locked behind capstone skills so they don't unlock too early and require significant point investment. Given I have been the only play tester, I needed this input so it is greatly appreciated.

Capstone Skills: I think this is where alot of the flavour will come from, but likewise I don't want the skill trees to mean nothing. I am not a fan of exclusive skills - one skill locking out another - but flavour wise I am happy to look at making the options broader to adjust the difficulty. I won't be able to cater to every taste, but I should be able to give degrees and levers to adjust it. They are just there for when the final skills in every branch has been maxed. Still a placeholder, at some point maybe they will unlock after certain skills have been maxed, at that point it will need a bit more direction.

Inserters: I noticed this and it's on the list, fast inserters are better that bulk inserters which is not where I want it to be.

Esc to close: Seems logical, I will see if that can be caught with a key press and not bring up the pause menu.

Invests per click: This is a overhang from my testing, I wanted to be able to quickly invest points. I will add those as options, but not remove the buttons, I think for visual access it's useful.

XP Curve: Yes, wildly overdone at this point. There was a time where even placing a blue print gave XP so slapping down a massive blueprint would give alot of skill points. I like your idea of adjusting xp to give more for longer crafting items, I will take a pass at this later and see how it looks.

UI: There is probably a bit of refinement required, due to only me using it I have flown through the last few builds and will generally miss alot of nuances now, either blind to it or not looking at that thing for the iteration.

Overall: Some great suggestions, really appreciate them, I will have a look now.

Maybe i should have write all of this as separate posts, so it's easier to track and I will definetely do it more concisely in the future, but I decided that it would be hard to decouple some things, and it's better to make one long and somehow structured post, than spam with dozen of small ones.
I have some ideas to suggest, but some of them may sound ridiculous or just don't go well with your vision. Just a heads-up.

I'm fine with however they come, just happy someone wants to have a bit of input. Created a post (more for my tracking than anything) to capture stuff I want to do but may require a bit more effort.

The "Invests per click" amount part is obsolete. I think it's better to:
"LMB = +1"
"RMB = -1" (yes, it is a request for a decrease-level feature)
"Shift + MB = ×5" — depends on LMB or RMB to increase/decrease
"Ctrl + MB = max" — depends on LMB or RMB to increase/decrease

The minus points was going to create a bit of an issue as it required a tonne of other stuff to be registered. I can look at that again in the future, but changed how the skill points can be assigned with 1.8.6. A free reset skill should be enough for now, Could maybe do reset branch? but then that would have interact with keystone abilities. Basically, a can of worms at every stop.

Sooner or later there will be an (optional) cost to reset skills, but I will bake this into the mods options to allow for all playstyles.

Reset one branch will be good, for now. Resetting all skills is a bit tedious to test

Ultimately, resetting/changing won't and shouldn't be "free" outside of the options I will add to support it if/when the free option is removed.

Resetting any branch would require a reset of the capstone skills, which isn't too bad, I wouldn't want to add checks in to see if they where active, just a straight reset as a cover all.

I can see the use case as the player moves from mid to late game and want's to min max a bit.

Realistically what I see is a "Tribute Chest" that will pay for resets, but for the next few iterations - if implemented - may just be a reduction in total xp earned, arguably the easiest root to take. Pay exp to reset.

Some things in the mod are still debug options, the reset skills being one of them, how that works in the future probably needs to be added to the list of things to refine. You're in early doors with this mod so there are some things are will be tedious that won't exist on the final version. I will try and get some point rebalancing worked in.

Now, if you think the mod will benefit that option (free respecs), I am definitely open to challenge. When the button goes it will be made an option anyway.

I have mixed opinion on "not free" respec in general, not particulary in your mod.

First, i don't personally like "not" free respec. The only thing it does is prevents player from constantly switching between most apropriate "build" at the moment. In rpg game that makes sense so it strong vs one enemy and weak vs other, which creates unique gameplay situations. But in factorio such skills are just upgrades like technology. It's hard to imagine situation, where you want to respec some tech to gain back science and invest it into something else. The only thing for now is military perks, because it's not used all the time. This will probably become wider problem after more "optional" perks will be added, but IMO this is no priority untill then.

Second, even in more final form the most used purpose of respec is testing. Playes, that don't know your mod will want to test different builds, see different perks (for now each perk has too long description, so it takes long time for that matter to get what exact effect will be gained), and it's really bad to punish that. And the bigger your mod will become, the more needed that will be.

Third, respec for "just more xp" is boring. Maybe it will be ok when more automative ways of gaining it will be introduced. I could suggest a tech or an item to do that, but for now your mod is not rely on that at all, and I'm not sure that it is a good idea to change that. But maybe ot's ok.

Perhaps I think let it be free and cross that bridge when it will treat a problem.

I guess I don't want the mod to get confused which it is in a dangerous point of doing.

I have given it the cheat tag, so realistically it should be no hold barred, it's not something I am sold on.

With regards to respecing I have just added a few new options to reset only the current tree rather than just respec everything, it may ease it a bit until point assignment can be a bit more dynamic. Again, these options won't ever be removed, either be a turn on/ turn off setting - if at all.

Either way, that it far far far down the road before I even consider it and will likely change my mind many times in-between. For now I want to get the skill points and skills at a good point and that is going to take a while.