By that I mean a bad faction that throughout the game winds up being the best hope for the future?
You get direct control over the institute in the end.
They have the means to cleans the Commonwealth and expand across the country.
They have fresh food and water at all times.
They have the ability to repopulate the world with animals.
They have the ability to rebuild infrastructure in the surface.
They can provide security for all on the surface.
All this takes is the PC making the decision.
IMO I don't see how anyone could side with the other factions. The Institute is everything the world needs and with the right leader can change the wasteland.
It would be a shame to see the Institute's destruction being the canon ending.