Well, 200+ years is a long time, and even then we still know very little about the commonwealth and the insitute. All of our knowledge comes from a couple of NPCs in a sidequest, it may feel shoehorned in because the lore around it hasn't been well developed yet. But then, I dont think it is shoehorned in at all. What we know about the commonwealth in relation to the insitute is that the commonwealth is a hellhole whereas the insitute has advanced beyond the pre-war tech. I think the contrast and the conflict between the haves of the insitute and the have nots of the commonwealth surrounding them is very interesting to explore.
There is still very little to go on, however, so what we may know about these places could be completely different by the time we see Fallout 4 for the first time.