To your point about he gets beat, so does Pistorius.
http://www.sentientdevelopments.com/2008/08/michael-phelps-natural-transhuman.html
Here's what Phelps has going for him:
• Most people have a wingspan that matches their height. Not Phelps. He may be 6'4" tall, but his arms extend outward to a total of 6'7".
• The average shoe size for a person the size of Phelps is 12; he wears a size 14 which gives him a 10% advantage over the competition.
• He also has a larger than average hand size which allows him to move more water.
• Phelps is double-jointed in the chest area; this enables him to extend his arms higher above his head and pull down at an angle that increases his efficiency through the water by as much as 20%; this also allows him to have quicker starts and turns.
• He has proportionately short legs relative to his long, powerful trunk; this large upper body is the engine that powers his long arms. Moreover, his unique physique reduces drag through the water and allows for maximum propulsion.
• Phelps has a greater-than-average lung capacity allowing him to execute his underwater dolphin kicks longer than the competition.
• He has a genetic advantage that causes his muscles to produce 50% less lactic acid than other athletes. This means he can work at higher workloads for longer periods.
• With a low body fat of 4%, he is better able to convert his effort into speed.
And you can also do some quick searches to find studies Phelps has been in and various testing he's had to do.