Some good points. Not to say that Phelps is not an absolutely incredible athlete; just that there a few other athletes that I would consider to be even more impressive I'd agree that Bolt is superior to Phelps just due to the amount he gapped the field in the 100 meters and due to the much larger field of competition in track. Also, Jesse Owens was probably even more decorated than Michael Phelps in his day. Michael Phelps only won one of his races by .01 seconds and most of his races were somewhat close. There are several other swimmers (Like Ryan Lochte) that are very similar to Phelps, but Phelps was really "on" during the 2008 Olympics. Also, many of Phelps' medals were from relays where he did not necessarily have the fastest split.
Actually, while Phelps was the most successful swimmer at the Olympics, I would actually argue that Tracy Caulkins may have been an even better swimmer, although she did not perform very well in the Olympics mostly due to the prevalance of East German Doping, and the 1980 Olympic boycott. Methods of testing for doping were probably not as advanced or thorough as today. Caulkins has been the only swimmer to ever hold American Records in every stroke.