To me the big differentiator between UA & AA is the Economy Plus section on UA that will make your ORD and SFO flights tolerable when the upgrades aren't there. Plus you can buy an E+ access pass to get you in while you earn status.

You should also check the BOS-SFO schedules; I think UA may have a 2-3 more direct flights than AA. They're about the same on ORD.