Much depends on what factors are important to you. For example, If it is non stop flights to your most common destinations, I would pick an alliance that has the most number of airlines that fly non stop. If it is the quality of the in flight service and seats, then pick an airline/alliance that best matches your needs, even if it involves a stop enroute.

It's probably best to pick an alliance that best suits your needs, as the benefits will be usable across all partner airlines, rather than being restricted to just one airline. Again, depending on where you want to go, it's not likely that a single airline can meet all your needs. Once you have settled on an alliance, then I would look at which airline has a frequent flyer plan that best suits your needs. My gripe with BA is the very high additional fees on reward flights and limited seat availability in higher classes.