It's understandable that nobody's picked up the baton here, unfortunately Alpha Protocol failed as a game, and people don't generally draw inspiration from failures. More over, even if the ideas are taken up, they're a ton of work for an experience that people aren't currently crying out for - if only because we're all used to game responses being limited to binary morality checks, and optional love interests.
But screw that. That way lies stagnation, boredom, and madness. Any RPG or adventure designer without a copy of Alpha Protocol and a notepad with its name surrounded by little hearts is an RPG or adventure designer not doing their homework properly. Like Vampire: The Masquerade: Colon: Bloodlines, Alpha Protocol is nothing short of a treasure trove of ideas and unspoiled systems just waiting to be cracked open and presented as new innovation.
Whatever game finally picks up the baton won't, and shouldn't just copy Alpha Protocol. It makes far too many mistakes, many of them obvious, and anyone repeating them would deserve all the face-slaps in the world. Luckily, the good bits and the bad aren't intertwined, and the fact that Alpha Protocol didn't live up to its potential doesn't mean other games couldn't on their own terms. Even if one only pulled off its tricks half as well as it did, though, it'd still have twice the reactivity that any other RPG is likely to offer in the next couple of years. I'd like to think that counts for something.