My opinion is that, if Obsidian, or any other RPG developer ever attempts a Spy RPG again, they should focus on building a spy. Put different choices in how you develop an ultimately stealthy characters: social (disguising/acquire info etc.), hacking, traditional etc., drop stuff like the weapon skills and reduce and change the pace of the combat. The obligatory bosses were just the icing on the cake of something that really didn't feel (gameplay-wise) like a spy experience. That said, despite the fact that it was very unfocused and had some bad art, Alpha Protocol's strong points made it a very rewarding game.
Plus, martial arts were cool.