in the change logs there were alot of optomization bits and pieces... no idea if they are expansion pack only, though.
ya, diplomacy's ai is signifcantly better than vanillas or entrenchements, although they still love to kill themselves on starbases.
the cobalt sounds different in vanilla. (didnt they go through like 3 versions on that for some reason?)
pirates are 1337 hax in diplo.
siege frigs are more powerfull in entrench and diplo
a few of the abilities are different from vanilla to entrench and diplo.
there are definatly differences besides the obvious expansion pack things.. but generally you really have to dive deep to find em.