Tony and Ed pretty much nailed it on the head. San Jose isn't too great in and of itself, but it's really a pretty good location to reside in the Bay Area just because of how easy it is to get to the other parts of the bay. I went to high school in Los Gatos- it's really nice aesthetically, but living there is beyond expensive and if you're not half of an old white couple, you'll probably get sick of the place really fast.
When it comes to the music, I don't really know what you'd want to define as a "scene." If you mean that the bay has a ton of really amazing bands spanning a really good variety of genres then sure, we have a great scene. For an already experienced musician, this place is great- people are in a ton of different bands simultaneously and are generally all really tight with one another. Sadly, turnouts for small shows anywhere in the bay usually suck regardless of the genre and it doesn't help that those great bands almost always play 21+ shows. That may not be a factor on your end, but all ages shows are often pretty depressing up here. In a way, it's almost like the shows played by the really great bands here (Slough Feg, Hammers of Misfortune, Cormorant etc) are really done only for themselves and their friends who want to hang out and get drunk, not the fans who actually love their music. The young thrash bands who play here get the shittiest turnouts though, and they don't support each other one bit. The old veterans from the '80s are always a good time to go see anywhere in the bay though, and you're bound to run into a few legends if you go to enough shows. All the Profound Lore bands tend to have cool shows as well, even if half of the audience are fucking hipsters (Agalloch and Yob come to mind).
To me, a good "scene" means both camaraderie between the artists and unity and dedication from the audience- the bay is missing the fans who are willing to go out and support fledgling bands and give up what they define as "good music" or whatever the hell. Honestly, when I started making friends at shows here I thought the scene was amazing, but then I saw that people were forming cliques for no good reason and that would actually affect turnouts up here-it was like these guys were in high school all over again. New bands practically don't stand a chance here unless they somehow align themselves with the whole John Cobbett gang or kiss enough promoters' asses.
Sorry for the rant, but I just felt like I had to clear up the whole "bay area music scene" deal. Yes we probably have the single most awesome collection of bands in the world, but it doesn't mean much when the fans only appreciate them through their recorded works.