So let's say you are thinking of supporting the Institute, and finishing the game with them. They seem like the best option at first glance.
They have what it takes in terms of knowledge and resources to be the future of mankind.
HOWEVER:
- they are responsible for killing your spouse and, without apparent reason, everyone else in vault 111
- they replace innocent humans with synth copies, humans which are after used as test subjects for experiments such as FEV (for what purpose?)
- they are belligerent, most like the Brotherhood, and don't seek compromise
- they created new life and consciousness, but do not respect or value it, they don't have empathy even for fellow humans since they use humans in horrible experiments, like Vault-Tec / Enclave
- not to mention that for the leader of this faction, YOUR SON, you were just an other experiment. In all his wisdom, he decided not to save you, but to let you out from the vault to see if you would make it! Towards the end he also have the nerve to order you to kill your friends (Railroad and Brotherhood), people who have helped you so far, while he did nothing (or worse) for you!
- as a proof of their failure in their twisted logic, "Father" has made a copy of himself, a lesser self, since a synth is just a tool in the Institute's views. So his synth copy is in a way the future of the Institute and of mankind: the humans from the Institute failed at being human (see above), similar to those who started the war, and passed the trial to their next gen artificial humans, the new Tin Men of Oz who will, in their turn, have to look for a heart.
So think again...
P.S. The Institute is very much like the Enclave, but they are dressed in white lab coats, not in black power armour. To bad the game doesn't have options so you could change their ways even after you are Director.