I agree with Elim on that, there are far too many stories out there which are based on things like, Destruction Of the federation and against all odds such things.... To me that kind of story is just too unbelievable. When set in the star trek universe.
Well you can still have that, just with a less well known foe, which makes it a bit harder to guess what they're going to do next and more of a challenge.
Now that I like. Is there any ships for them though? I know someone was making a Sona ship somewhere.
There is a whole fleet of Breen ships on BCFiles (sans HP's unfortunately) that you could probably use with the modellers permission.
The Sona only has an old out of date Battleship (on BCFiles) so you could probably do with a modeller on your team to build the missing stuff.
I'm sure you can get an HP'er (sorry I'm fully booked at the mo. ;) )
The Alliance thing was only an idea, there's plenty of other ideas you could use;
Maybe two of them are at war, and you have to pick your way between them to complete missions?