I would just like to thank GreenFlag for putting together a great scenario pack for Factorio. I love story driven missions and as much as I love Factorio it is definitely one aspect of the game that is missing. So it's good of you to fill that niche.
I have played the first 4 missions and am currently working through the 5th. I see that you are intending to make more and I look forward to those too. The missions thus far have been well paced, not overly difficult or time consuming (I reckon I have spent about 15-16 hours not including mission 5). Personally I wouldn't care if they took longer. My only gripe and it's just a pet peeve is I don't like timed missions, Mission 3 had me worried with the 5 hour time limit and the limited resources to get a factory going and research Military. In the end it only took me about 2.5 hours to complete (although I did have some possibly game breaking help, but more on that later).
Mission 4 - bases. I like the organic design of your bases in this mission (and so far in 5) , that said it can be a little confusing to figure out where to put the resources you have to go out and collect. Less experienced players might have difficulty figuring out what goes where. I would suggest replacing the inserters on the chests with filter (or stack filter) inserters set to the appropriate resource. When ALT is pressed it would just make it that little bit more obvious for what goes where and reduce contaminating the belts. Same applies to Mission 5's base too.
Mods.
I usually run a heap of game changing and QOL mods, obviously I turned most of them off but I did keep a few and here's how they went.
Spidertron Start - Causes immediate game crash on load, obviously conflicts with something, suggest adding to incompatible list, probably game breaking.
Tiny Start - Small Armour with Equipment grid and roboports/bots. Very handy in early game. Great for clearing trees and repairing your car and buildings and building smelter arrays etc. Worked fine through missions 1-4 but failed to load properly on Mission 5, possibly due to spawning inside a train. I can live with out it but is a nice to have option.
RPG - System. I like this because it increases stuff like crafting speed, movement, mining and combat abilities. You have to work for it though. That said in missions 3 and 4 I really leveraged the combat abilities which made your missions much easier. As I said earlier for mission 3 possibly game breaking for your intended difficulty.
Jetpack - haven't used this one in game (it requires rocket fuel so not researched that far in any mission thus far) would break the game in missions 3-4 because you could just fly into restricted areas/behind enemy lines.
Mission designs and objectives are good, mission descriptions could perhaps be a little clearer but are adequate, unique base designs are intriguing, Would like a little more latitude to explore your bases, particularly in mission 2, Maybe just add a few more radars so people can look in map mode. You built it so let people see it.
Thanks again, if anyone else is thinking about playing this go and do it, it's fun.
PS I'll report back later on my thoughts for Mission 5.