If you're looking for elite upgrade availability, sometimes joining a program from a carrier that isn't a hub may help, especially if you'd only be in the lowest-level elite tier. You're competing with fewer elites for a limited number of upgrades.

However "where do you fly on paid tickets" plus "where do you want to fly on free tickets" are probably the most important factors, if your goal is maximizing miles for future rewards. The other thing is award availability. It may be anecdotal, but it seems easier to find saver (25,000 mile domestic, 50,000 Europe etc) tickets in UA, NW, and AA's programs than it does in CO "NonePass" or DL. I don't have any experience with US's program.

Just make sure you don't spread miles across multiple programs in one alliance. You probably know that already, but just join one program out of NW, DL, or CO and use it for all three; join one out of US or UA and use it for both.