I've stayed at the Prescott, Palomar, Monaco, and Harbor Court so far. The room we got at the Palomar was our favorite of these (even if our view was into the Old Navy downstairs). I think the Harbor Court only has one suite, so upgrades there are probably harder. The Harbor Court has a very nice view of the Bay Bridge though.

The Prescott's extended happy hour was awesome, but the hotel definitely has a bit of a worn feel. You know how some showers have a thing that you pull up on the bath faucet to activate the shower? Ours came completely out and created a little fountain.