Yeah, the Institute not having any sort of plan really hurt the faction.
I mean, the Think Tank was also doing science for science's sake, but that was the point, what they did was useless at best, highly dangerous at worst, because they were already assholes as human beings, and now they are half insane on top of it all.
The Institute never gives this vibe. The narrative very much treats them as a valid faction that has a point and a plan, except it never bothers to explain it all. Why did they spend a century churning out hundreds, if not thousands, of Super Mutants? No reason. Why even make Gen 3 Synths if they are so anti transhumanism? Why even interact with the surface world if they think it's hopeless up there? Why even send Gen 2 Synths to patrol the surface and kill anything on sight? ''Because we can''? That works when you're designing a one-off villain to a DLC, not the faction that is arguably the most central to FO4's plot and world building (such as it is).
Cripes, even Fallout's very own Nazi expies had a plan. Even the Mutants in Fo3 had a plan. The Institute apparently does mad science for the sheer lulz of it.