As Zap Rowsdower said, a spiritual successor would be great. The subtle link between the gameplay and the effects on the story was brilliant, you almost forget the game system and the mechanics. This discretion, this attachment to the role play, video games developers should take care of and improve this.
But there is no need of Alpha Protocol 2, I think. Too many endings, that are a perfect conclusion. And sometimes, you just have to imagine : the mysterious and secret atmosphere of the game is important.
I rather prefer a new edition of Alpha Protocol with gameplay mechanics improved and menu glitches fixed. ^^