I think the main reason is that the area is getting more and more expensive. People don't want to move there because a 2BR condo is around 400-700k and the taxes are in the double digit k's. Also the expense in commuting is getting worse and worse.
I think that if hardware companies and software companies wish to stay afloat and do good, I suggest they relocate to a much cheaper area, or they are going to continue to get burned.
Another positive they can get from relocating is it will create jobs in a new area and boost another area up. However, the area that the companies do move to will need to plan the upsurge-economy very well so they do not suffer the same fate as the bay area.
Also since the bay area is so expensive and exclusive to rich people it is deterring many young and fresh minded people from moving there, thus the amount of fresh blood people is decreasing, thus the old mentality is staying in and the area is stagnating in talent becuase noone from an outside area is moving in. They are trapping themselves in the bubble that they created. If they lower costs of living for everyone and get thier heads out of thier asses then the area's situation will improve.