Scott--
I'm not sure I would carve out time from a cross-country trip to play Harding, if a number of any other possibilities were realistic options.
I think has been an interesting exercise for those of us former and current Bay Area residents to play the renovated Harding, to compare it to the former incarnation. I'm not sure I would term it a "missed opportunity", however, because I'm not sure there was ever any realistic chance it would be ever be anything more than what it is now--what chance was there with the City admin. and PGA Tour involved?
Is it currently better than what it was 4 years ago? I would say yes...however, I would think that before the decade is out, there will be more similarities than differences between the newer Harding and the older...
I would put in another point for the Presidio. Quirky, and somewhat repetitive in parts, but "location, location, location"--I've been getting e-mails about special greens fee pricing that brings it back closer to a more realistic figure...
Lastly, for "in the City-limits" golf, that is truly San Francisco and no where else, let's not forget the wild, quirky, irritating Lincoln Park. I would argue that it has more of a "sense of place" for an urban course than anywhere else. Not a great golf course by any stretch of the imagination, but there is no mistaking exactly where you are!
Peter