Couldn't agree more. To some people, Beth is in a lose-lose situation if they don't introduce the 100% perfect (to them - which is different to every person) new organization.
I'd like to see it be the Commonwealth. Lots of opportunities for quests and mystery. Who is an android, who isn't? Should you help them break free or help control them? Hell, you could have the player BE an android.. but maybe you don't know it until later which adds a whole new dimension!
No one is expecting perfection from Bethesda; especially not the people who are hardest on them... trust me on that one.
Ideally Bethesda should introduce a major faction that is both developed, and fits in with the retro-50's setting. The Commonwealth has loads of potential; the only questionable aspect is the androids which resemble something from 70's or 80's Sci-Fi more than they do 50's sci-fi. That ship has already left the harbor though.