Matthew Rorie has also said Alpha Protocol will display the most typical RPG elements including NPC's interactions, even sleeping with them. I understand player will be able to build complex relationships then. Is it correct?
True. Even your hated enemies will see value in allying with you at points depending on your personality and mutual goals, you can reason and blackmail with masterminds, and even cause several antagonists to re-evaluate their goals. You can have romances, "no"-mances (our anti-romances, and boy, can some of the women hate you), suffer loss, make friendships, and even bask in the crazy joy being completely unpredictable and fucked-up with some of the folks in the game.
...
You said that the moral ambiguity of Alpha Protocol will be closer to Fallout 1 and 2, which is very promising. Could you please explain how is this system being developed?
Alpha Protocol doesn't attach a moral absolute to the main character - instead, we track the player's attitude and individual NPC's perception of the player's morality and ethics. Basically, the player gets judged by the NPCs, but his morality isn't a number or scale attached to him personally.
Basically, the world paints you as a saint or demon - but even that's too simplistic for people's attitudes in AP, since each of them has a different perception of right and wrong. Each NPC brings their own morality judgments to the table - so saint/demon can translate into sympathetic, worthy of respect, friendship, object of romance, aggressive shithead, etc., but in terms of you judging yourself? Hell, you're just doing a job. You know why you did what you did to get the job done, the world be damned.