I'm pretty sure any suggestion involving letting people choose or even influence the bonus ship type is going to be rejected, as stated in the FAQ, one of the reasons for the randomness is to "force" players to use other play-styles, or not use the bonus ships at all. You can find their stance on this at
http://arcengames.com/mediawiki/index.php?title=AI_War_-_Design_Complexity#Why_Does_The_Game_Force_Variety_On_The_Player.3FWarning: long philosophical rambling ahead.
I will be completely honest. I think many of the design philosophies behind AI war need some rethinking. Note, that this will be no small change, but many of these complaints are actually complaints about things stemming from the very goals of this game.
Such as forced variety. While done right, it can make the game fun, when you make it a central pillar, gamers will try to find a way around it.
We, as gamers, like "the optimal strategy", which in many cases means focusing less on the random aspects (aka. the variety) and more on the static aspects (like star-ships, the triangle ships, etc). I don't take it to quite this extreme, but from what I have seen, alot of "pro" players do. And even if you aren't a pro player, this design philosophy seems to clash a little with what many RTS players try to get out of a game. Forcing variety, thus interferes with this process, thus it can interfere with the "fun factor". Generally speaking, for many players,
some of these noble, unique design philosophies make the game a little (or in some rare cases, a lot) less fun.
So yea, this tension is sort of caused by a fundamental difference in game philosophies. Thus, there is no easy answer about how "fix" this. In other words,
even if everything is balanced according to the game's philosophy, some of the more "annoying" aspects players have been complaining about since forever will still remain, due to differences in philosophy between he devs and "average" RTS players.
Also, I am not saying the Arcen should just completely change their design goals for this game; I love this game to death. However, maybe you can make some of the more controversial goals (read, goals that can reduce "fun") a little less central to the game. Again,
there are no easy answers for these types of problems. For example, I like the heavy focus on variety. But making it such that "every time I start a new campaign I am presented with practically a fresh game" seems a little too far. (quote directly taken from the FAQ)
Woa, really started to ramble there. I'll shut up now