There is a lot of subjectivity when you put superlatives on any athletes, but we all can agree that what Phelps accomplished in Beijing puts him in a leage of his own.

 But, if your argument for him not being the greatest Olympian is because he won that many golds only because he was a swimmer, then that does not make much sense. We are talking about the greatest Olympian NOT the greatest athlete. The rules and the categories of the Olympics are already there. So, if he has more gold than anybody I don't see why he can't be claimed to be the greatest (or one of the greatest ever) Olympian. 

I agree with you that Guo could have won more medals had there been more events in her area of expertise. But the FACT is there weren't, and this is Olympics. So, she isn't the greatest Olympian. I don't think I will disagree with you if you claim her to be the greatst diver yet. And, since Phelps won the most golds in a single  OLYMPICS, not just among swimmers,  I don't see why he can't be called the greatest Olympian until someone breaks that record. You can argue that Olympic is biased towards Gymnastics and Swimming when it comes to rewarding, but that's how Olympics have been for the last however many years.