The last few years it seemed to me that Alaska sort of abandoned the Bay Area, except for their expanded services from all three airports to Hawaii, which has been a godsend given the withdrawal of AA (and DL's attempts to fly people on red-eyes back to SJC).
Not really. AS serves GDL, SJD, BOI, EUG, RNO and SLC from SJC, along with Hawaii and their hubs. That's not "abandoning" the Bay Area (and they are adding SAN and SNA in a couple months).
It will be interesting to see what they do with the SJC focus city once the merger has fully proceeded (where they are a solid #2 to WN). That being said, WN flies a good schedule from SJC, SFO and OAK, and BUR, LAX, SNA, ONT (and soon LGB too), so I suspect AS is going to try and imitate that model of using secondary airports and main airports in California, rather than focus everything at SFO/LAX.