I might be able to say more if you give some examples for things that have been bugging you about this mod? Or if there are specific things you're looking for advice for?
Generally, one of the big "oh god" parts in this mod is the code for probabilities. That's just, one big mess and there's probably plenty of edge cases where it doesn't work all that well.
The other thing i know isn't great is the overall balancing because the randomization isn't properly normalized. By that i mean, the default setting isn't really mathed out to on average be the same difficulty overall (ie increases in costs balance out with decreases); it's pretty much just with some experimentation and guessing. Which is really a good summary of the mod overall; it's pretty jank. If you can do it better / more elegantly, i'd definitely encourage you to do that in your own mod instead of trying to keep compatibility between the mods. Yes compatibility would be nice, but i don't think it's so important to sacrifice quality for it. If you do make it compatible, i would be happy to include for example more randomizations into this mod as well though.
Generally, some important things to keep in mind is both scaling for your code (if you've looked on the source code for this mod, you'll know how much changes one needs to make; so make sure you have a good workflow and reuse code as much as possible), edge cases (a lot of properties have boundaries defined in the factorio API you'll encounter; i've had a lot of bug reports for things like beacon ranges getting out of bounds for example because i didn't check all those in advance). And to be VERY careful about how the data is organized. If you look at randomization of turrets, you'll see there's a really ugly if-else chain because the data there can be arranged either as a list, or a list of lists - in two places. So you need to catch all 4 different possible cases because mods can do it in different ways because it's not strictly defined by factorio.
Also think carefully about how you want to make it customizable. This mod is a bit of a mess between the different blacklists that exist, and the settings menu. I tried to make it very modular because that's how i personally like my mods and i want to allow people to play the game in the exact way they want, but the more options you provide the more important it is to think about how you're gonna organize it or it becomes an inscrutable mess.
Other than that, i also still would like to randomize more things and i have some specific ideas too but just haven't gotten around to / haven't had the energy to do it, especially since i stopped playing factorio. That's the other thing that does bug me apart from the probability stuff and general jank-ness.