Of course, there is a ready-made, in-universe explanation for why you could make an obvious, direct sequel that has zero references to Alpha Protocol:
"Alpha Protocol? What's that?"
Alpha Protocol was designed to be shut down and reformed; all the characters were intelligence assets using assumed identities. You could write a brand new spy game with the exact same voice actors, using a brand new set of names that makes perfect sense in continuity. Mike Thorton is dead; Miguel Torres lives!