There's always some talk about stuff and for sure a few dodgy things happened in Beijing (so many in gymnastics too). But Phelps won it plain and simple, thanks to far too much practice. I am glad he got it too, he's a very nice guy and suffered (still does, of course) from ADHD and as you can see has a bit deformed face. His sisters also have ADD or similar. Phelps used to get picked on too but never did anything back and once he started winning the bullies from the past would approach him and be all nice, and Phelps' mom told a pretty cool story.
There was a meet when he was 15, after he qualified for Sydney 2000, and a guy walked up to him and congratulated him and asked if he remembered who he was, to which Michael said sorry, he couldn't, but when the kid walked away his mom went up to him and said Michael did know the guy. But Michael replied something like "yes I did, but I didn't want to give him that accomplishment".
Now that shows some maturity right there, in my opinion. Anyway, there are plenty of good stories around him if you bother to find them, he's a good person to carry the honor of the medals.