-Alpha Protocol has a New Game+ mode of sorts. When beginning the game as a Recruit, you have no skill points at the start; you only get them when you level up. It will be tougher to play through the game this way, but you get extra "Recruit" dialog options (down on the dialog stance system) and when you finish the game you unlock the Veteran class.

-The Veteran class allows you to start off with 3 skill points in every category and also get additional "Veteran" dialog options.