That sounds a lot like Alpha Protocol, Obsedian's spy RPG that was mediocre at best. It came out a year later and sounds very similar where your Agent could be "suave" like James Bond or a neck-snapping ninja like Jason Borne or a gun totting lunatic like Jack Bauer. Here's a quote from wikipedia regarding the game:
"Alpha Protocol features numerous characters with whom to interact. Conversations occur in real-time, giving the player a limited amount of time to respond at key "decision points" during dialogue.[6] The dialog system in the game - known as the "DSS" or Dialogue Stance system[7] - allows the player to choose from three different attitudes, or "stances," when speaking to an NPC. Obsidian has said that these options are based on the personalities of the "three J.B.'s": Jason Bourne of The Bourne Identity novels and films, James Bond of the eponymous film and book series, and Jack Bauer of the television series 24, although the game itself does not use these names. During dialog sequences, the player will be able to choose from options like "professional" (Jason Bourne), "suave" (James Bond), and "aggressive" (Jack Bauer), sometimes with a brief description of the dialogue choice (such as "sarcastic") taking the place of the general stance. A fourth, "special" dialogue choice is also sometimes available." (Note: while it may seem that this is only regarding the dialogue, anybody who's played the game would see that there were skills needed to upgrade that focused on gadgets (Bond), martial arts (Bourne), and guns (Bauer).)
While this probably isn't the same game as the one Bioware was working on, they seem eerily similar. Either way I doubt it was Rockstar's Agent, since the discription of Bioware's spy RPG doesn't seem to mention the era it was meant to be set in, which seems to play an important role in Rockstar's game. Also since this thread has been quiet for the past couple of months (or since the announcment of the PS4), isn't it likely that Agent has been moved to next-gen consoles?
