Definitely good and evil factions. The Fighter's Guild and Mage's Guild would be good, and the Dark Brotherhood or whatever an assassin's guild would be along with the Thieve's Guild would be evil. And add the Imperial Legion as a joinable faction again! The Legion was one of my favorite questlines in Morrowind.
I'd rather have shades of grey then good and evil to be honest. i feel its more important to have the characters choice.
it works both ways for most anyway.
Thieves Guild, stealing is bad, so was Robin hood the bad guy?
Mages Guild, Magic is good, but necromancy is bad, (i know its band, but it might be possible in this game)
Fighters guild, depends who you fight for really....
Assassins guild, depends on who you assassinate... (ok, i realise that is pretty weak, and the assassins guild is pretty much as evil as it goes, but i never said my plan was bulletproof...)
I hope that these 4 stay in, same as i hope the arena is there in some form.
I'd also really like more factions to join, especially some kind of militia group, such as the imperial legion in the days of morrow wind.
Maybe a bandit group, who also operate a few pirate raids, maybe a religious cult, a town council, a band of mercenaries or a renegade legion.
To be perfectly honest, the possibilities are limitless, and i'd be abit disappointed if they didnt include more factions.