I've said this before: The big problem with the institute is that they have on coherent plan. Their goals and methods change with every new Director. If they had one, clear mission statement, and every Director worked toward that one goal, they would be more of a force to be reckoned with. But, instead, they flop around like a fish out of water, for the most part. Sure, they have synths operating on the surface, and they still replace people from time to time, but that seems to be more of a "gathering resources and information" play than anything else. Mayor Quimby is a Synth, and his sole purpose for existance seems to be to control the flow of information in Diamond City (Piper) and report anything of note back to the institute. And not much else.