Really, each alliance has a decent number of flights out of RDU. AA and DL both have fairly large operations (remember, they have most of the gates on concourse C), and US actually has a decent operation with their frequent flights. Personally, I chooses UA over US, since about the only thing I haven't gotten on US over being one of their elites are upgrades (I live in GSO which US dominates, so I have to fly them regularly). I have gotten great last minute deals on UA and DL ($210 to ONT one weekend buying the day before). I don't have any experience on AA (out of GSO, I can't fly to MIA or DFW just to connect up to the northeast for work, takes too long), but I have fallen in love with *A cooperation compared to ST.
Though I know a lot of people here will trumpet the benefits of their program, it really depends on the level of service you can get to where you want to go.