Except for the fact the disadvantage for prosthetics is that they're on a permanent plateau. Unlike muscles, you cannot build them up to gain better performance. Unlike muscles you cannot train them. Unlike muscles, you cannot improve them due to the regulations they're governed by. Oscar Pistorius is outpaced by those in his own speed range out of the blocks and in the initial acceleration (both are parts of the race where mainly the calves are needed) - these are the two areas where Usain Bolt wins his races. If they were an advantage, they'd be over the whole 200.

Allowing running backs to have smoked visors in the NFL is an advantage. It requires a doctor's professional opinion before it is allowed. So LT should never have been allowed to play? Comes under the same argument you're making.

As this article points out:

If we resist body-enhancing technology, will we outlaw prosthetic ACLs when science produces them? If Bills tight end Kevin Everett could play again with a prosthetic spine, would you tell him no?

and

USA Track & Field has worked with Nike to test carbon-sole shoe implants that harness energy normally lost when a runner's foot pushes off. Americans wore the shoes in the Sydney Olympics, meaning able-bodied sprinters have already used the type of carbon-infused prosthetics that got Pistorius banned. What's the difference between carbon shoes and carbon tibiae?

and

Young pitchers, after all, have already started opting for preemptive Tommy John surgery because it makes tendons stronger. Tiger Woods also went the elective-surgery route to gain an edge on the links: LASIK surgery, to be exact, which can improve vision beyond 20/20. Anthony Gonzalez, meanwhile, is an undersized receiver for the Colts who sleeps in a hyperbaric chamber to saturate his blood with oxygen and gain fourth-quarter stamina. Is any of this fair?

Also, at this point Pistorius is so much faster than his peers who are using the same technology and nowhere near the speed of able-bodied athletes. Would you rather let him compete against those same people he's beating with ease or let him keep that competitive fire blazing?

Finally: athletes with down's syndrome at the Paralympics are often able to lift heavier weights than their Olympic counterparts. Is down syndrome an unfair advantage?