You're going to need to look carefully at where exactly you're going, and how often. You'll also need to decide if you care about things like international upgrades. You may also wish to look at the financial health of your carriers.

I fly out of SEA, and I was more or less in your position a year ago. I chose AA because a) they had a plat challenge that could get me status fast, b) they seemed to serve international routings well, and I like that EXPs could get upgraded. AA seems to quite often have fire sales on SEA-east coast routings, which I really enjoy. But my situation is slightly different in that I live for travel of all sorts to all places, and I do it on my own dime.

AS has a very nice program, at least on paper. I recently got comped to MVP Gold on the basis of my AA flight record. One killer perk of AS's program is the ability to make free changes to purchased restricted tickets. I used this feature last night without a problem for an upcoming trip. The only open question about Alaska's program is whether the competition for seats will deny you upgrades. AS's elite thresholds are relatively low, and you may find yourself competing with more folks for free open seats. On AA, if you're EXP or even just PLT, there often aren't too many pople who can "beat" you to the upgrade. My upgrade record as a PLT was exceptionally good; as EXP I expect it will be even better (just crossed over.)

Nutshell: if you think you'll be flying mostly domestic and AS can take you those places, and your due diligence suggests good upgrade potential, give AS a go.

If you care a lot about international upgrades and/or certain cheap east coast routes, AA may be a better bet.

For myself, I've made both AA EXP and AS MVP Gold, and I will be trying to matain status in both programs. We'll see.

-KF