I was actually, at one point last year, thinking of a game where the main character would be an experienced hacker. The game would have a similar approach to games like Alpha Protocol, in which you actually learn things related to hacking and otherwise throughout the story.
I wasn't thinking too much about the main character, besides the few facts that he's got a bunch of good friends, and contacts around The US, and he'd be able to use their resources at any time throughout the story. He could then maintain a relationship with is old friends while meeting new ones, and reputation would have a large play in terms of standing with someone. For example, taking out a guy in a particular way could impress some, and others would be thankful for you because of the hit.
I was even going as far as thinking of a Parkour element, mostly because I thought of it was an interesting way to get around during certain missions. Similar to Deus Ex, it would give the player options on how to complete the mission, and Hand-To-Hand combat would be a lot more fun if the character you played as was more agile than most others.
Well, looks like Ubisoft beat me to it T_T