It depends how big it gets really, 4 is a good starting point so people know its not a standard 2 faction MMO with imbalanced pvp and has the option for more. Extra factions should be added as the community expands though so that we don't end up with a load of ghost factions. It would be awesome if it got so popular that they could add every major faction as a playable one without spreading people too thin, though I guess as you say it could get a bit crazy having so many factions all fighting each other, especially if they all ended up in 1 spot.
While seeing any faction, including the Adepta Sororitas, would be cool....it makes more sense to add one that isn't directly related to another in game so soon. Tau's the best idea for the first expansion race, Necron need to be NPCS.
I think a mixed Imperial guard/Inquisition/Sisters force could work fairly well, and I´d definitely like to see it.
I'm torn between the Guard (my army so a little bias ) and Tau. The only problem is finding a way to keep the Guard effective for gameplay without making it seem too much of a spit in the lore's face. Tau on the other hand pretty much wage war in the way this game is supposed to play so they're a perfect fit.
I think it probably will be either IG or Tau, but I'm leaning toward Tau because IG have so much more obstacles to implementation. Adding Tau is just adding one more race, their troops having a distinguishable style (long range), average power level, and no affiliations with any other faction. Plus, mechs. With IG, you first have to deal with their basic troop being much weaker than the average of almost every other race, and more numerous. Then you have to deal with how they interact with the space marines, who are supposed to be allies... Would they be set against each other to keep the balance? And on top of that, all the IG tactics are inherently kind of spammy for a video game: tank spam, artillery spam, infantry spam, rocket spam. That's just how they fight. I wouldn't envy the devs trying to do an implementation like that. I figure they'll take the easy way out and stick to Tau.