Hmm lots of possibilities, but what the hell. Wild and baseless speculation can be fun!
The Institute wishes to maintain: 1. Their level of influence, 2. Their independence, and 3. Their intellectual purity by admitting only select individuals into the Institute. Due to the recent Brotherhood's interference, they've started increasing the production of terminator-like synths (non-human looking ones) for defensive and offensive situations.
The Brotherhood might be split into two factions similar to FO3 except much more focused within the main quest.
Brotherhood faction 1, possibly lead by Arthur, wishes to increase / continue to increase their numbers by recruiting outsiders. They wish to control / take down the Institute for the good of the commonwealth and to ensure their advanced technology doesn't wind up in the wrong hands.
Brotherhood faction 2, wishes to maintain their purity by refusing to recruit outsiders and keep membership in the Brotherhood to almost entirely descendants of those families who originally started the Brotherhood. They see the technology of the Institute as a means to make the Brotherhood strong once again without resorting to diluting their membership.
Main quests will involve conflict: 1. Within the Brotherhood, including faction 2 having infiltrated faction 1 to some extent, 2. Between the Brotherhood 2A. as a whole or 2B. each individual faction and the Institute, 3. Between the Institute and the Commonwealth People, and possibly 4. Between the Brotherhood 4A. as a whole or 4B. one or both factions and the Commonwealth People.