There aren't a whole lot of things I would change. Maybe a few.
1) Go with writers original idea to have the Dominion be like a totalitarian Federation. Many different races, not just three.
Exactly how am I supposed to picture that? It's totalitarian in that the Founders have absolute control and subjugate other races, yet "federated" in that every member of every subjugate race still has an equal opportunity to reach a high office?
I agree seeing an "anti-federation" would have been cool, but it would have required inventing a lot of new races, including costumes and makeups, most of which would have been on screen only for a very limited amount of time, and even in our Federation, there seem to be way more humans in Starfleet than you'd realistically expect for a true team effort ....