Here is a list of all of the races that will appear in the MLP: FiM Mod/Campaign, and their respective faction names:
Equestrian (Galactic Equestrian Alliance): You play as this race.
Canid (Kingdom of Canidra): Initial enemy.
Mobian (Galactic Mobian Alliance, Sonic the Hedgehog's Race): Probably will end up in a crossover campaign.
Seedrian (Empire of Green Gate, alien race from Sonic X): Probably will end up in a crossover campaign.
Terran (Galactic Terran Alliance): Will cross over with the Campaign, this is Freespace.
Vasudan (Parliamentary Vasudan Empire/Galactic Vasudan Alliance): See above.
Shivan (???): Primary antagonist.