Hmmm....I'm no expert on SAN in particular, but that seems like it might be a UA/CO fit. (Star Alliance)

Houston is a primary CO hub.

SFO is a secondary UA hub. (Lots of flights, but not quite ORD or DEN.)

I think if you definitely want to fly out of SAN (and not LAX), you'd be mostly looking at one-stop to get to a lot of East Coast markets, but UA through DEN or CO through IAH would be as logical as anything else. (LAX of course would give you more nonstops and might make AA/Oneworld more attractive to you as well.)

Personally, I've always accrued miles on UA. The biggest "pros" for UA are Economy Plus and very affordable systemwide upgrades if you are a very frequent flier (100k miles per year). A downside to UA is that they have been known to filter out the best partner awards - even when the partner airline has made award seats available (referred to often on the UA board as Starnet blocking). CO has pledged not to Starnet block after they join the alliance, but other than that I know little about them.