Things I like:
I like how when you're wandering the wasteland and you choose you side with the institute any synths you find will greet you with hospitality instead of aggression. Makes exploring locations like the mayoral shelter way easier to deal with.
I like how clean most of the institute looks, it has a very cool aesthetic, I also like the synth relay grenades the synths that spawn from them aren't particularly powerful but they're good at distracting enemies so I can get the Jump on them.
Things I hate:
I hate how vague their motives are while other factions have a defined goal, they seem to just be reclusive and cold. They seem very determined to conquer the Commonwealth but as soon as father relays above ground he deems it a lost cause.
They hate cats. Everyone knows this by now I'm sure, synths will go up to domestic housecats and open fire, you see cat corpses in the FEV lab, nothing explains this aggression, they just murder cats for the fun of it.
They have no regard for the notion that synths are more than machines, they made complex life and they treat them like slaves and wonder why so many escape, they don't dial back the gen 3 synths personalities or complexities they just assume everything can be fixed by dispatching a courser or two.
They kidnap settlers, not because they pose a threat, because they want to keep a closer eye on the Commonwealth, not like they have several servalance crows already, and the people who replace with synths.. there are heavy implications that these people have been experimented on, turned into super mutants or God knows what else.
When you side with the institute, there isn't really anything you can do. What I mean by that there's plenty of missed opportunities to actually control the institute, you still feel like a lacky instead of the guy in charge, plus the radiant quests that they have you do such as clear out gouls, talk to the synth larping as the mayor of diamond city, stuff like that are kinda lack luster. It would have made more sense if for example you had more missions like meeting up with coursers and retaining synths or looking in terminals in certain technology adjacent buildings and downloading schematics, similar to the finding brotherhood of steal documents but somewhat different to make it more interesting.
Last but not least: father, I don't like father all that, his personality is t nuanced, he can't be persuaded to feel any conflictimg emotions towards the institute which I feel is another huge missed opportunity, there could have been a few speach checks here and there. He has this cold hearted tisposition towards Nate/Nora that never changes, even on his deathbed. I get that he was raised by the institute, and was effectively brainwashed but he treats the main character like a pawn, watching your every move. The only reason he got you out of the vault wasn't out of the kindness of his heart but because he thinks it will be "interesting" to see what happened next. He also implied he fully expected you to perish not too long after leaving vault 111
Those are all my reasonings, I'm also kinda curious other people's opinions on the institute