I’m a full time motorcycle commuter in the SF Bay Area too.
I think the main down-side to motorcycle commuting is in depreciation of the bike; especially if you buy new. You’re going to put a lot of miles on that bike in a relatively short time and here in the U.S.A. where motorcycles are largely considered toys, that matters a lot in resale value.
So! You either replace the bike in two years at, say, 25K miles and take the depreciation hit for a new one, or, you keep it and run it into the ground, because if you keep it for another couple of years and put, say 50K on it, you might find it difficult to sell at all; even though it’ll probably run to over 100K if well maintained (and not written-off of course). Just don’t tell your insurance company that you do anything more than pleasure ride a couple of thousand miles a year or they’ll crucify you. They don’t consider the mileage when you make a claim anyway in my experience.
I too mainly do it because it’s fun and quicker and if I weren’t commuting by motorcycle I’d be riding BART (it’s a train folks!), so depreciation wouldn’t be a part of that equation.
These are just my musings on the subject and I may be wrong, but it’s the way I currently see it.
I think the take-away from this is not to commute on an expensive new motorcycle.