A - Big advantage UA in terms of flights/routes and aircraft types.
B - Not sure if it matters. Both award full RDM and EQM on leisure fares. Both allow domestic upgrades off of any fare. International upgrading varies - not sure about the specific differences. United tends to tie a lot of its bonus mileage promotions to Q fares, which is a mid-level coach fare. Might be a slight advantage to AA here...again, not sure on the finer rules of international upgrading.
C - Certainly a lot more 1K's than EXP's in the Bay Area. But...more widebodies on UA so more upgrades to go around. I fly to SFO about 3 times a year and I have had decent luck as a 2P (soon to be 1P). I'd give the advantage to UA simply because when you get upgrades, you will get better seats. When you don't get upgrades, you'll at least have E+.
D - I'm not sure exactly what types of miles you are looking for besides status and promo miles. I would think that Mileage Running would be easier on UA simply because you have more seats to pick from and therefore a greater chance of finding deep-discount fares on off-peak flights.

Only thing I don't know is if UA customer service at SFO is high-quality, because they feel it is a valuable competitive market, or crappy, because they have a hub mentality. The only thing that has scared me off from UA in the past has been abysmal customer service in certain locations. I'm back with them in '06 because I have little choice, and to be honest I haven't had any recent, major problems with them.