PossibleCabbage
Vault 22 Survivor
I hope Bethesda didn't take the criticism of the Brotherhood in Fallout 3 being too goody-goody too harshly and have them become Enclave: Part 2.
They can make for good villains, but they shouldn't do the Snidely Whiplash thing.
I think between New Vegas (which they didn't make, but at least probably learned a thing or two from) and Skyrim that they realized that "having multiple competing factions none of which is clearly in the right, and let the player pick which one they would prefer to back" is a reasonable way to structure one of these things. So you'll probably have neither the Institute nor the BoS being the "good guys" or the "bad guys".
It will probably be a "control and safety" versus "freedom and potential" values clash.