1. Super Mutants: We know theyve been loose for almost 200 years on the East Coast so it isnt suprising that we see them in Boston. Hopefully we have a leader figure that will justify why so many are present in Boston and why they didnt completely overrun the Capital Wasteland in 200 years time (given the Super Mutants high numbers, the CWs low human poplulation, and Lyons BoS inability to make any real gains.. I feel this should be addressed) because BoS doesnt do it.
2. Enclave: We see Enclave armor in the Bethesda video showcasing armor modification, so it's safe he Enclave will be present in some form in Fallout 4. And because the story takes place at the same time as Fallout 3 we can [possibly] justify a population with them having not yet reported to Adams Air Force Base and been annihilated. Or they are the scattered remnants who got away; and, while on the run are still incredibly dangerous because of their technology and training.
3. Brotherhood of Steel: Dont need to say much here, but cant either because they certainly dont seem like the White-Knights they once were in Fallout 3; and no info regarding the story has been given. Given we see the PC blow up a BoS Vertibird and shoot a rocket at a power armored foot soldier.
Additional Note:
Id like to see a return of the Swampfolk in the swampy areas of the game. They were certainly tough enough to grow their territory to Boston, given the impulse. Bad stat implementation or not, I loved the danger they presented and the creepiness delivered by them.