What were the long-term effects of finishing the game with one of the four factions? More specifically I was wondering about becoming allies with the Institute. Will the people of the Commonwealth be unhappy and hate me? What about your companions?
This question is for all of the four factions (Institute, Brotherhood, Railroad, and Minutemen), but I'm really more interested in the effects of ending the game with the Institute.
I have limited experience since I'm only on my second playthrough however so far I have observed -
If you join the Minutemen you'll end up allied with the Railroad and will end up destroying the Brotherhood of Steel and the Institute.
Additionally, if you've progressed through the Minutemen missions (upto and including retaking the castle) then during the mission where the Institute attempt to "invite" Wallace to join their Biosciences team it will be the Minutemen that respond to Wallace's distress call (thus giving you the opportunity to talk them out of it). If you haven't joined the Minutemen, the Gunners will turn up to respond to Wallace's call for help. Progressing through the Minutemen story will also result in numerous groups of wandering Minutemen patrolling the wastelands in addition to unlocking artillery.
If you join the Brotherhood of Steel, you'll declare war against the Institute and Railroad while being allied with the Minutemen.
If you join the Railroad you'll be allied with the Minutemen and destroy the Brotherhood of Steel and the Institute.
If you join the Institute you'll be allied with the Minutemen and destroy the Railroad and the Brotherhood of Steel.
After completing the storyline allied with the Institute, groups of synths start showing up all over the commonwealth announcing that the Institute is now in charge - they'll also set up a variety of checkpoints and roam the wastelands killing mutants and raiders. The various companions I used during my playthrough didn't mind that I had sided with the Institute however I expect that Deacon and Danse might (since you destroyed their factions).
Regardless of which choice you make,
"Father" will die, however the cutscene will be different if you aren't allied with the Institute. If you attack the Institute you'll lose that as a fast travel location. Any factions that you wipe out will not be available for missions after the final cutscene.
Actually you can have the Minutemen and the Brotherhood of Steel work together. In my playthrough I initially joined the Minutemen. Then when the Brotherhood asked me to go towns and get them "compliant" I only did the initial town Sanctuary. This flipped it and turned me back on the Minutemen's side.
In the ending, the Brotherhood decided to align themselves with the Minutemen and "use them as cannon fodder" to take out the Institute in order to minimize casualties to their own men.
