I stay at various Marriott-related properties in San Francisco about twice a month. I have the best luck with room size, treatment, and upgrades at the San Francisco Marriott. The Renaissance properties don't like to give upgrades very often.
The problem I have found with the SF Marriott, though, is that they've shut off some of their floors due to low occupancy, so from time to time they've not been able to give me the type of room I've been booked in. The good news is that all but one of those times they've found a full suite for me.
The SF Marriott is a MUCH nicer property than the Fisherman's Wharf marriott. I recommend that you go with this property.