I really feel like it might feel better to be able to take that 15 minute bike ride then bike ride to the bus, etc. Plus, I feel like I might lose study time and enjoyment time if I need to wait and ride on Caltrain each day. Maybe I should just get over it?!?!
There's not necessarily a one size fits all right or wrong answer here, mostly I think those of us mentioning other locations are encouraging you to keep an open mind while doing your research, and look into some non-PA options as well. Then it will be a matter of doing the math for all the possibilities you find, money vs time and hassle. (Caltrain is mostly pretty good, I used to take it from Sunnyvale to San Carlos every day, and actually kind of missed the "me time" for reading/knitting etc when I changed jobs and downsized my commute at the time. VTA light rail, in my limited experience with it, is painfully slow and would be a tougher sell.) Lots of other cities here already do have things like the farmers markets, active downtown areas and such, and it seems as it's getting more popular more of them are heading that way too.
Also, in terms of how fast prices and things can change around here, you have quite a long time until your move, so specific rents for your actual situation will be tough to pin down. If your SO isn't in the tech industry, you may be wanting to root for another tech bust to help you out. As others have mentioned, housing will be the biggest hurdle, if you can sort that out everything else is pretty easy. Good luck, and check the meetups section when you do get here, there are actually quite a few mustachians around here, in spite of the high COL!