I agree, Ubisoft should really consider cleaning up the Ghost Recon lore. That way we won't have to deal with arguments about who the Ghosts are.
Granted I still sort of want them to be Green Berets, doing what Green Berets do best.
Hell, I even think an open world Ghost Recon game where you nurture and assist a guerilla force would be pretty neat. Ubisoft loves having dynamic elements in their games, why not a Ghost Recon game with a dynamic campaign that reacts to your actions?