I think people would be able to help you a little more if you could go into a little more detail about what you're trying to get out of your FF program. Specifically, what kind of relative importance do you place on benefits of elite status (upgrades, mainly), as compared with the ability to use your accumulated miles.

My guess, based on what you've said, is that United probably is best for you -- their miles are certainly the most valuable among NA carriers -- but anecdotal evidence suggests that upgrades are becoming hard to come by, even for 1Ks. One other thing to consider is that Amex MR points do not transfer to United. That could be fine, maybe even a benefit, as you'll quickly have a lot of UA miles and the MR points would provide a form of diversification.