I actually think the alliance thing would be rather restrictive, preventing the kinds of complex relationships that develop between empires in SE4 games, where empire A is at war with empire B and partnered with empire C, but empires B and C are partnered... when I played MOO2 I almost always rejected alliance offers because I just knew my "ally" would come to me demanding that I declare war on one of my other trade partners, and if I said no the treaty was automatically broken!
MOO2 actually had an adaptive AI, by the way - it gradually borrowed ship designs from the player!