2) From what Chris seems to have in mind, the goal doesn't seem to make a monstruously upgraded ship that has little in common with the base one, rather to enable "base" designs to tweak, and evolve somewhat if necessary against whatever new tool the AI unlocked. I like this vision, a lot. It would not revolutionize the role. You'd have "fighter A" and "fighter B", but both would recognizable as fighters, following the idea that mk1 and mk2 are fighters despite having wildly different stats.
The problem with this is that there's no way to represent that visually, and uniformly. "Fighter A" and "Fighter B" would still just look like "Fighter", basically. The Mark system actually didn't do that: There were 5 marks, EVERY ship that had multiple versions used the exact same 5 symbols (making it super easy to look at and grasp, and this was very, very important) and each mark ONLY represented an increase in base stats. None of them were "Well at this mark you get 50 armor, but at THIS mark your speed increases and you don't have the armor, but this ship over here does different things at each", which is what you'd get with this new system, and is a huge part of the problem. With the Mark system, you always always knew that II was better than I, and III was better than II, and so on, each meaning pretty much JUST increases in HP and attack power and general basics... very easy, and totally uniform across all ships. "The next level is better and there are 5 levels" is the one and only thing you need to know about the Mark system. When you unlock your next level of bombers, they're just outright better than the last, period. But there's no way this new system could do any of that, considering the absurd variety of possible upgrades. It couldn't be uniform, and there'd be too many things to remember because each is not necessarily better than another within the same set of upgrades for a ship, and trying to represent it visually would be a bloody mess.
Having all sorts of different upgrade effects without an easy-to-instantly-spot visual effect in a game as complicated as this one is not a good idea; that's why the first game didn't do this whatsoever. This goes for player ships and/or AI ships.
It works in something like StarCraft because the game as a whole is completely different. StarCraft is EXTREMELY focused on micro and small battles between unit groups, and things like build order. AI War, on the other hand, doesn't even remotely come close to playing whatsoever like StarCraft; you've got LOTS of different maps to deal with all in one campaign all at the same time on an overall galaxy map, there's asymmetry between different groups, there's tons and tons of special structures, there's just outright TONS more things and much greater complexity from a non-micro standpoint. There's an enormous amount of things to deal with. Wheras in StarCraft you tend to be super-focused on A: your base, and B: a few groups of units.... and that's it. The complexity doesn't come from the same source types as it does in AI War. And lastly.... you don't get even remotely close to the unit scale with StarCraft as you do with AI War. 200 units in StarCraft is quite a big amount. In AI War, it's hardly anything at all... With so many possible things all over the place to look at and mentally grasp, it's important to keep each individual one as distinct as possible, PARTICULARLY from a visual standpoint.
Ugh, if I keep going on about this I'm going to make less and less sense... sorry if this all seems more garbled than usual. Posting kinda close to bed time here.