All they will really need too do is focus on either continuing Mike's story or go the assassins creed route and introduce a new protagonist whom is connected too Mike. Also make the story longer. Much much longer. I can wait till 2013. Just give me a game I can waste my time in. Waste it away like nothing in the world is wrong. Also focus more on developing relationships (both the casual and romantic) with the people in the world around you. So that it really matters if you **** someone off or not. I love Alpha Protocol. I bought it and I was immersed fully. I just think it should be longer when you guys make the sequel. And also, a game series that is selling poorly or failing should not be given up on. Especially by Sega. (Imo Sonic) So give Alpha Protocol another chance!
I liked alpha protocol a lot, it actually got me into the neo-rpg type games. I ended up playing mass effect after it, but I actually preferred the interaction and human element of alpha protocol to mass effect's.
If not a direct sequel I do hope that we will see a game with the same or similar core mechanics and amazing attention to detail coming from SEGA.