I actually favor the idea of multi race fleets with certian limitation. First the team must declare a primary race, which will determine whether they are Alliance (Fed, Hydran, Gorn, Mirak) or Coalition (Klingon, ISC, Lyran, Romulan) as well. Second they may only take 1 ship from an allied race in a 3 ship fleet. 2v2s require you to fly just your primary race.
This preserves a certian amount of the historical flavor, but allows for a little more flexibility and balance where certian races don't match up well against non-traditional enemys and such.