2. Muni does not need more money. SF does not need more money. SF's budget is twice that of Idaho's, and we have far fewer people and far less space than Idaho ( http://www.sfweekly.com/2009-12-16/news/the-worst-run-big-ci... ). Look no further than the ridiculous extension of muni from China town to downtown to see a clear indication of how funds are being completely misused. No one wants to fix the budget problems in SF and its so much easier to just blame whoever happens to be successful at the moment.
3. I'm not sure I disagree with your third point at all but also don't understand how its a negative thing. You are describing normal competition between companies. I can at least provide one piece of information: I used to work in the South Bay and hated the commute and would do everything in my power not to ever do it again, bus or not. So there's plenty of incentive to stay and work in a small company here, I assure you. Do you see lots of small companies running buses (honest question, I'm simply not familiar)? I seem to just see the flipside happening: more small companies simply being in SF.