For me, it's always been UA. My pattern is similar to the OP's with a particular emphasis on BOS-SFO (family in Bay Area). I also fly a lot of other places a lot. I have always had several nonstop options to the West Coast when it was absolutely necessary to get there NOW (e.g., on a freebie). UA now flies four NSs each direction, down from 7-8 each way, as I remember, before 9/11. If they expand again, I would anticipate building that route up again. BOS-NY, and up and down the East Coast, we have US, on which you earn all UA bonuses, and have access to their club if you belong to UA's RCC. UA flies the East Coast, but it's a connection. And BOS-ORD, well, it's practically a UA shuttle.

One other good thing re the BOS-SFO route: During the off-season, BOS-OAK itineraries go for ~$225 RT, as long as Jet Blue is doing it. And UA matches Southwest's PVD-OAK/SJC fares, if not their terms.

My main issue with UA is that, eastbound from BOS, it's always a connection (through IAD). AA is better for nonstops eastbound. UA discontinued their BOS-LHR on 9/12/01. Given their stated strategy to cater to the type of traveler who would fly this, could it come back as they build back? (For you, this might matter if you want to use a freebie to vacation in Europe, but that would be a rarity, probably?)

I have a big issue with AA's MD80s. More than other mainline planes, they are a mail tube in the sky. As AA has committed to all-Boeing, this will phase out, but it sure isn't happening fast. At the same time, UA flies a lot of A319/320s, a slightly wider, more enjoyable plane than the 737. Truth in "packaging": UA is flying more and more CRJs on longer and longer routes -- not necessarily out of BOS, though. At the same time, they are using them to expand, out of IAD, to more and more tobacco-state routes.

More than you ever wanted to know...