I personally think that Institute is the best way, when you do missions for them you see why they replace certian people, for example seeds that contains radiation in one of the farms, or they are looking for supplies which they need and obviously everyone wants supplies, thats why they need to fight for them using their synts. Also they mentioned that they tried to install goverment above ground but stupid freaks was against it because of superstitions. I always hated fact that I couldnt join Enclave, like in F4 where you are able to join institute even if you are enemies at the begining. Also if there will be Enclave ressurection in Fallout 4 DLC, I think that alliance between Institute and Enclave is very probable.