You can post multiple ideas, as I am about to do below. I am going to express every single possibility there is, even if the proof is miniscule.
China - China might just be a faction. It DID become the new world superpower; perhaps, even, it will slightly take the place of the USA?
USA - It went into isolation, but it just feels like it's not Command & Conquer without it. It might take its rise again, or....
UN - It was a small, unplayable faction in the regular generals that appeared during certain missions, usually as the color Cyan. For instance, In Generals, GLA Mission two as the convoys. It might also be part of the EU.
NATO - Yes, i did research. I never actually discovered this in the game, but it apparently had some interaction in the generals series. It's a supposed part of the EU.
Russia - Lazy as I am, i didn't really look at this. However, almost 60% of the people on this 'third mystery faction' topic on different sites think it might be on this. It did have quite a lot of involvement in games, anyway. It also was a planned faction, one of the vehicles being a Tzar Land Ship
Khan - Research evidence again. It was planned to appear in Generals 1, but was later replaced by China in the final release.
Africa - Some people may think this is crazy, but it was planned as a faction in generals, but was discarded.. Two of the vehicals (weren't really vehicles, but were classified as such) were the Lion Tank and the War Elephant. Even crazier to most people, a planned infantry for it was called a 'Genetic Horror'. I wouldn't be too surprised if it was or wasn't put it. It would make a good antagonist for the reasons of banding, but other than that, probably not.
And thats al. If i find more, I will post more. Please post your ideas on what you think will appear!
Heh heh... EA Games never knew there was a Naval general...