I'm not a student at either school, but I did apply to both last year. You mentioned that you'd like to get back to California- I suspect you'd be in good company at MCW. I recall that approximately 25% of MCW's students- i.e., half of all the out-of-staters- are from California. Also, I have the impression that MCW has a slightly better national reputation than UVM- in part likely because it's a larger school with more alumni, more research facilities, etc.
As far as your concern about UVM's 1.5 years of basic science, I wouldn't worry about it at all. Step 1 is now more clinical than ever and UVM students will quite likely have an advantage over students in more traditional curricula. I'm at a school with a traditional curriculum and I can tell you from my own experience with shelf exams that they are VERY heavily based on clinical vignettes. Anyway, most of the stuff tested on Step 1 is path, pathophys, and pharm, which are all things that you'll get lots of exposure to during your 1.5 years of rotations. There is comparatively little anatomy or other first-year material on Step 1. I wouldn't let that factor influence your decision too much.
A final consideration is cost of living, which is utterly outrageous in Burlington. It's tough to find housing and the prices are through the roof. That's surely part of the reason for the high debt load carried by UVM grads. Housing near MCW is much more reasonable and relatively easy to find.
With all that said: I absolutely LOVED Burlington. I loved the lake, the mountains, the skiing, the cool little shops downtown...it seemed like an absolutely fabulous place to live for an outdoorsy granola type like myself. Matter of fact, I plan to apply there for residency. Though MCW is in a nice suburban neighborhood, it's still Milwaukee, which IMHO doesn't hold a candle to Burlington.
Good luck with your decision- sounds like you can't lose either way!