I think Alpha Protocol is a full fledged RPG, with some of the most impactful roleplaying decisions I've ever seen in a cRPG.
I think that´s a valid point, though personally when I describe a game as a fully fledged cRPG it means that it, among other things, comes with at least partially open world design and a party of characters. It´s certainly a pretty meaningless descriptor when it comes to telling anything about a game´s actual quality.
Point is, C&C is it's strong point, but it's lacking significantly in other areas. If it wasn't then it would have been a lot more popular around here.
It likely would have, but I think it´s actually a fairly popular game around here - at least to me most of the people who played it seemed to like it. It also ended up at 29th place in RPGCodex´s top 70 list and that in my opinion happens to be a very good list.
I´d add that while its combat gameplay is somewhat lackluster (though personally I wouldn´t categorize it as bad since I actually rather enjoyed going through the game´s levels and I don´t thing its worse than in, say, Bloodlines), the game delivers a kind of experience that can´t really be found anywhere else so, at the very least, it´s not a redundant game.
Also, while it doesn´t excuse the game itself, a quite interesting point is that, according to an interview with an Obsidian dude, the way character stats affect shooting mechanics was SEGA´s mandate, not something Obsidian wanted to do.