@solost - Glad you got to the end and were content with the ending you chose.
@Mahaloth - I’ve (in the thousands of hours I’ve played) done every ending, but was most frustrated with the institute ending, in that, if I’m the head of the institute, why can’t I put together a more peaceful solution? But as said earlier . . . there are mods for that. 
Lore and world wise though, my default is the BoS ending - because, and forgive me a minute if I sound like a BoS Zealot, this is absolutely one of the technologies that is too dangerous for humans. Not because synths are inhuman, or robots, or anything of the sort, but because humans cannot use this technology ethically.
MINOR SPOILERS FOLLOW
The institute flat out replaces people that disagree with them with synth slaves, and there is a strong argument that they do it to their own people as well as their enemies. Eventually, you are going to end up with someone unethical enough to replace everyone at the top with synths and have a total dictatorship that will likely collapse when some mastermind dies.
The railroad has zero issues with wiping synths for their own good. Even with permission, the single example you meet in game has no where near the mental maturity to be making that decision. The railroad may have good intentions, but it is killing the person who gave consent, and creating new personas that may or may not be capable of making ethical decisions going forward. A situation that would likely get worse in a post-destruction of the Institute storyline, because otherwise, what purpose would they all serve. Not to mention, on related notes, the fan theories about PAM (fun, look them up!) and how Arcadia in Far Harbor is run (not saying more there, because, big spoilers).
Lastly, the minuteman? They were an utterly failed experiment long before the MC showed up. They depend upon a single person for guidance and to do all the work. The minute the MC retires or is gone, they are likely to break up into massive factionalism again. And considering their intense manpower shortages, I see no way they wouldn’t use the Synth technology ‘to protect the commonwealth’. Possibly for the greater good, as it were, but it would still be an abuse of what may be free-willed beings, and likely to end up with yet another gang of extortionist overlords (just like the BoS tends to be).
Okay, rant off.
Honestly, I always wished that there was a way, after saving Virgil, to bring him back to the Institute and put him in charge, along with a few others that still have the basic moral underpinnings to function as part of an open society. Most Fallout societies are scavenging or getting by on restored tech without looking forward, or looking to avoid the dangers of the past. Getting someone to think beyond returning to the past (the NCR is going forward to the past with all it’s corruption, expansionism and oligarchy at near lightspeed) or protectionism with exception for the chosen elite (BoS) is a worthy goal. For all its flaws, the Institute is one of the few that seeks to do so.