San Diego flies under the radar, probably a top 10. Water or access to it is important, IMO. LA is impressive, but the natural surroundings is lacking. Not too many downtowns are located on a bay front with ocean cruise liners, air craft carriers, a NAS, Coast Guard helicopters and an international airport adjacent to a beautiful skyline.
I don't mind the height limit too much as downtown continues to fill in with numerous high rise projects instead of one or two monsters. Super talls are only good when viewing from far away.
1) NY
2) Chicago
3) Boston
4) SF
5) Miami or Seattle