All this could be said of House as well, but when he is out for himself it is somehow to the benefit of humanity yet when the Institute is out for themselves (or science for science sake) it can only be bad?
House largely ignores the common man, if not outright uplifting them if they prove useful. He lashes out against antagonistic forces that are either already working against him or no doubt will, but The Institute actively targets, kills, replaces, experiments on, and undermines/destroys entire civilian settlements. They're hardly equivalent, and one is much more incompetent than the other.
Science for science's sake is all well and good up until it winds up negatively impacting the whole for the benefit of the few. And what have The Institute even created that's worthwhile? Human clones that they insist aren't human but clearly are, that they can't control effectively and whom they abuse for no discernible reason, even though Gen 1/2's don't have pesky free will and do all the same shit modern synths do without any of the pesky morality involved? Laser weapons that are objectively worse than anything you can find pre war? Clean hallways? They can't even cure Father's plot-disease.
The tech used to create synths could, conceivably, be used to the ultimate benefit of mankind but they have no intention of using it that way. What has their science done to benefit anyone in The Commonwealth that isn't themselves? I'm genuinely curious because I don't think there's a single example and the game makes it pretty clear they're villainous in this regard, because they actively repress and kill everyone topside by either using them as a dumping ground for fucked up experiments that go awry or out of pure malice. We can argue over 'maybes' or headcanon until the fucking cows come home but the game makes no effort to prove they're anything but violent isolationists who harm innocent people above ground for nebulous goals that they don't even have a firm grasp of. You at least know what House intends to do, and it seems mostly good but with some gray morality mixed in. Which, hey, if we're arguing over which of the two has more moral grayness mixed into their bones then there you go.
The Institute is just a shittier implementation of the same concept. A concept Bethesda did much better in Far Harbor, if we were talking about the groups there I'd say there's more room for debate since DIMA is clearly just The Institute but with better writing.
Edit: Also I don't get the argument of "an unchecked institute" as the ending is literally your character taking control of the institute.
Do you really? You're hardly anything more than a figurehead, the board still largely does whatever it wants and you get to make no significant decisions regarding the direction The Institute will take going forward. Maybe if the game had some ending slides influenced by a karma meter or choices that you'd made leading up to it, we could assume that The Institute might turn it around, but all you get at the end of the game is an empty choice with no effect whatsoever to either ramp up synth production or focus on weapon manufacturing, neither of which seem like they have altruistic end-goals, and it's a choice presented to you by someone else.
When I mentioned an unchecked institute I was moreso talking about them acting with no antagonistic forces working against them, but still, I just don't see a player controlled Institute changing much, if anything.
