The service at Aqua has always been a little uneven [one waitress called my mom 'hun' and another waiter was a stiff-as-a-board relic straight outta the long-gone Charles Nob Hill] and the overall atmosphere is a little too stuffy for my tastes. These irrelevant points aside, I think the food remains quite good. Though its not quite at the lofty levels of its heyday a few years back, under a different chef, I think. I wouldn't say that it is better than Gary Danko across the board.
I like Aqua although there have been some inconsistent times.. I had lunch back in February and it was excellent. I ate there many times before hand and always pleased.
As far as service in general San Francisco would not be on the top of my list, I hope I don’t sound snobbish but having had impeccable service elsewhere regardless of the cost it can be a hit or miss here.
A couple of months ago we had a great meal at Aqua. I thought the food was as good as ever. The service was fine, but not amazing.
I'd say don't put too much weight on the Michelin Guide for SF, the timing and method of their reviews was called into question after several inaccuracies were discovered. Don't worry about parsing out the difference between one or two stars, or some places that got none.