First off, I love GCII, and I think DA is a great expansion pack.
But really, there is one thing about GCII (and, consequently, DA) that quite simply...bugs me.
It is the governments. They have no flavor, at all. It is completely linear. You start out with an Imperial system (even though the Terrans and Altarians are probably democracies), and you get a better option. It's not like Civ 4 (on a side note, I enjoy GCII more than Civ 4) where different government types have advantages and disadvantages over each other. As we all know, the Republic is better than Imperial, the Democracy is better than the Republic, and the Federation is better than Democracy. The only disadvantage to these newer systems is that systems will break off a bit easier.
In GCIII, I'd really love to see a more complex system of governments. But, once again, I love this game, and I think Stardock has done an excellent job.