My guess is that in Fallout 4 we'll be going up north a bit to see what the Commonwealth is all about. This might also be Bethesda's chance to introduce some new factions into the mix. We might also possibly deal to some extent with the Brotherhood and how they feel about Lyons' effective mutiny.
Indeed. I would like to know what happens to Elder Lyons. My guess is that, since Lyons and his people found Libery Prime, a prime and invaluable piece of tech, they will be granted clemency for Lyons' unique interpretation of the BoS mission. You'll see two divisions of the Brotherhood emerge. There will be the original Brotherhood, devoted to tech recovery and then there will be the Lyons Brotherhood, devoted to protecting and saving the people of the Wastelands.
Of course, it would be really cool if the next Fallout took place in another country. I wonder what post-apocalyptic London looks like? Or perhaps Rome? Paris?