The Six Million Dollar Man.
Keep the show a lot like the first season of the original, when it was still kind of dark and serious.
In terms of his "powers," instead of having a few limbs being bionic, I'd make his entire body augmented to support the bionic parts: a metal laced skeleton like Wolverine, nanobots in his bloodstream to sync his bionic parts (including the eye) to his nervous system, etc. And I'd give him a bionic "ear" that allows him to communicate directly with the agency and download information directly to his brain.
Then, like the original, I'd have him working for Oscar Goldman at a top secret spy agency, only more badass, making the outfit a cross between CTU on "24" and the agency on "Alias." But instead of just a secret agent I'd write him as more or less what a character like this would really be: a bionic assassin, near-terrorist, for the US government, taking on missions that the government can't handle by conventional means.
Each episode could be a one-hour action movie, with extended arcs now and then and a lot of ongoing subplots: one week they could have Steve parachute into Afghanistan to kill some Al Quaeda biggie, the next he would be sent in to rescue some hostages on a compound in the midwest.
Basically, I'd make him a bionic Jack Bauer.
Finally, in order to explain the title of the show, I'd establish that his annual salary from the government is six million bucks, and not what it cost to rebuild him.