Hopefully a game set in Legion territory would be set after Caesar's death so that we can see the Legion in the light of peace-keepers or as a necessary evil in a world without rules.
That would be a creative way to fuck with players as well, people avoid working for Legion because they were 'the bad guys' in New Vegas, only to find that they got an awful ending for siding with an opposing faction which didn't have the ability to bring order that the Legion had.
After Caesar's death, imagine if a more reasonable emperor takes place, guy that has other values, believes in hardcore democracy and all that. But since the Legion is dying because Caesar is dead, we have this civil war going on because Legionaries that had power (like, the representants of Caesar in some settlements) thinks that this new emperor is full of crap, and claim that they are the true followers of Caesar.
Some settlements thinks that the new emperor is nice and support him, others support the rebel Legion, some want full independence from all this crap and maybe we could even bring NCR to the table.
But here is the trick, imagine if NCR has failed big time, its all corrupt and full of mafias to the point its really a dictatorship of those who hold economical power, so then we would have the Legion with old values, Legion with new values, NCR dictatorship or a full independent region, that could be a new possible faction to be born, with different values from all the others, like some hardcore communist idea!
The independent faction could be a more "under the radar" thing at first, that would be building up as the plot progress with all the political disputes and shit throwing betwen these big factions.