Star Trek Online is starting out with two factions, the Federation and the Klingon's. Even though the game hasn't even launched yet, I think it is a safe bet that they will add a third faction eventually. Star Trek has a number of interesting possibilities, so which will it be?
Assimilate Ten Rats. Who wouldn't want want to fly around space in a cube? As they are likely one of the primary PvE enemies, it doesn't seem that they will be playable anytime soon. But you can get one as a part of your crew when you pre-order from Amazon.
Rules of Acquisition. I think the Ferengi would be an awesome faction, but their economic goals may not fit well into STO. I also think they may be one of the Federation races but that may have just been a dream.
Cardassians. I couldn't think of a good way to start this one. STO has released a screenshot of one of their ships, so they seem like they are in the game. Of course, they may be a PvE faction. They do seem like a good candidate for a playable race though. Always fun to oppress some Bajorians.
Ketracel White. The Dominion (shapeshifters and Jem'Hadar) would be interesting. I'm not sure of the full lore in STO, but they would seem like a good candidate for an expansion. It'd be interesting to see if they use the drug addicted nature of the Jem'Hadar.
Pass the Romulan Ale. The Romulans are probably my favorite Star Trek faction. Technically they are the 'dark elves' of the lore, but they don't seem to be super heroes like Vulcans. They are no friends of the Federation and the Klingon's, so they would be a great first expansion. Their ships look awesome, which should be the only factor considered :)