Right downtown it's not too dangerous, and there are some good housing options. And downtown is an easy bike ride from Temescal, Rockridge, the Piedmont Avenue

Right downtown it's not too dangerous, and there are some good housing options. And downtown is an easy bike ride from Temescal, Rockridge, the Piedmont Avenue area, the Grand Avenue/Lake Merrit area, or Piedmont (city), all of which are reasonably safe places to live (certainly on the same level of "safe" as you'd find in San Francisco -- Piedmont is probably safer, in fact). And all of those destinations are predominantly flat gradients to downtown (well, at least compared to San Francisco hills; it's not Kansas). San Jose, on the other hand, does suck to get to from the East Bay. Best plan is to avoid going to the South Bay, or to hope that your destination is within striking distance of the Amtrak station. Or to hope that they finally finish the Bart connection. I agree that Caltrain gives you better South Bay access; I'd be tempted to Bart in to Millbrae and transfer to Caltrain if I still lived in the area and didn't feel like driving. When I lived in the East Bay, I would end up in San Jose only 2-4 times per year, and I'd usually drive. On the other hand, I worked in San Francisco for over three years, and I never drove to the City once during that time; a mix of Bart and ferry trips (depending on where I lived at the time) handled my commute nicely. There's also a great start-up incubator (or at least there was) in downtown Oakland; a start-up that I joined moved in there for a year or so, and that made for an even easier commute.