Well, the only Alpha Quadrant power that isn't in the war yet that has appeared a lot are the Ferengi. And I don't think them joining would be all that impressive. So it had to be a species close to aliens of the week in any case.
That's certainly true. There's no real obvious choice. I guess that's why we ended up with the Breen. It's too bad, in a way, that there wasn't an equivalent to the Romulans available.
Edit: Regarding Sisko's mother being a Prophet, I've always been ok with the choice because it brings the non-linearity of the Prophets' existence into tighter focus than really anything did previously. I think that's especially important leading into the finale. Also, it gives the Prophets a tighter connection with Sisko, so his interaction with them can have an emotional element.