That's true.
I guess I would be in favor of, say, renaming the Fortress to something and fixing its issues, and come up with a 'staging area for attack' thing if anything, if my idea got support at all. I mean, Fortresses are basically massive gun batteries that can heal ships and move slightly... Not what I think of when I think "Fortress".
...the negative side to that though, is the idea that veterans are used to Fortresses, and don't want to be getting used to entirely "new" units that are just renamed.
If we must just stick with the basic model and not have anything fancy, unbreaking the bomber-only attack idea would be nice. I think maybe go for some kind of multistage attack. bombers survive the cannons, and go in for quick raids on those cannons to bring em down, before fighters swoop in and batter away at the hull, whose weapons they're resistant to. Or, better yet, Missile Frigates can outrange the hull's gun, but the cannons outrange the missile frigates. Just, something more involving than a "This ship beats the fortress" affair.
Regarding power creep, I kind of agree based on what I've seen, but I haven't yet experienced it. In fact, a lot of the game seems really reasonable when you aren't playing with minor factions. It seems more like the minor factions are what throw everything out of whack. To me, that's kind of okay, but that's just because I haven't had the experience with minor factions yet. I mean as far as I'm concerned, they're optional, and if they break the challenge, a good fair vanilla game against 10/10 will solve that problem entirely.
It's like... to use an unrelatable example, if you've played Super Meat Boy... Super Meat Boy has many unlockable characters. Almost any of them can be used to complete any level, and get full rewards from them. In fact, some characters are downright broken and completely trivialize the challenge of the game. I think this is okay, though, because the people who WANT the challenge will opt for Meat Boy. People who want to cheese things with double jump go for the Kid. People who want to teleport through literally everything play as Naija. I suppose the difference is, there, you have to earn the characters. In AI War, you just get super weapon factions if you want them.
I think a more organized discussion on power creep might be a good idea, but we need a good base line as for a "What should be balanced?" Obviously a game against the AI with everything including Hybrids on is entirely different than a totally vanilla game with only expansions and no minor factions/plots.