I think it's clear. Nobody likes the idea of putting the Rommies with the existing factions. NOBODY! NOOOOOBOOOODYYYYYYY!!!!!
So what's a somewhat REALISTIC way to put in a 3rd faction?
(Don't talk about species!)
1) The new faction has less levels. Whether you go from Cadet to Captain in one feel swoop like JJ-Kirk (and basically have Tier 1 then 4 and 5, no tween ones or something) or just start at Commander and go up doesn't matter (tier 4 and 5 or something). There's less levels. Perhaps 20.
Why you ask? It's much more realistic to make content for a limited amount of levels and ranks when there aren't as many.
You can make a third faction with depth, unique missions and really good. Just smaller. More compact. Easier to make. Just as meaningful and fun.
So basically the 3rd faction should have 20 or so levels. Enough real PvE missions to fill that content (maybe including Episodes). Tiers spread out or linear. The only reason I say they might be spread out is if you have a Cardassian or Romulan faction I don't want to see the Hideki or TOS BoP (C-Sore ) higher than Tier 1. And you can't have tier 1 in 20 levels if you don't skip up at some point. And I DO want those ships palyable. Just not at higher tiers. So maybe the faction might jump up like 30-40 levels at some point.
2) Because you level quicker (due to there not being as many levels) you'd ONLY be able to make a character of this faction if...
A) You pay into the C-Store (maybe)
B) You have a max level Fed or Kling character (or perhaps just one ranked up to a certain rank like Captain or Commander)
Quicker leveling would be unfair otherwise.
3) As long as there was enough PvE content for those 20 or 30 levels and enough ships and end game stuff (the same amount as the other factions) and a good story I think this would be the way to go with a 3rd faction.
So in short... Upon reaching a certain rank as a Klingon or Federation character you'd access the third faction.
This faction would have less levels but by the end would be at the same level and have the same access to end game.
Due to less levels it would be easier and more realistic to make content for it.
The faction would basically be a full faction as far as end game is concerned. And a few less levels wouldn't kill anyone.