I know the unit caps have been discussed to no end, but I'll throw in another suggestion regarding that.
What if there was a limit to the number of ship cap increases, and/or such building wouldn't be constructable by the player.
For instance, roughly one out of ten AI planets could have a special structure you could capture (just like ARS, etc), and it would either randomly (I like the idea of random, because it brings in that variance AI War is good with.
) increase the build cap of one of the player's available ship types by a certain amount, like maybe 20%, or the player could choose the ship type which cap to increase.
This would allow some variance in ship caps for each game, but wouldn't really be enough to make other ships obsolete, unless the player has some mad luck and gets same ship's cap increased multiple times, which in itself would be very unlikely, considering the number of ship types often available.