I actually toyed around with the ending of Infamous 2 and it can only go several ways. Cole, if in the bad ending, must be knocked out by some stronger conduit (or multiple conduits, which would work best as a seperate faction). He should be transported to the city his body is going to in the good ending. Amnesia would be Cole's main affliction in this story. That's one.
Another is that the player's choice is disregarded and one of the endings takes prominence albeit karmic choice. The good ending works well, because Nix, playing as Cole's romantic interest during the evil missions, can be seen as a reason for him to resort to the "good" ending (now in quotations, being no longer polemically good). Also Kuo is a *****, and those who tend to be immoral are often self-centered and apathetic to altruistic motives. If I had lightning powers and I was rockers I would never join Kuo to destroy/"save" the world. A big part of the following game would then be Cole exploring his real interests in love and whether he's acting out as a thug because of neglect, primarily from Trish in the original. Continuing from the evil decision is harder. There are ways of doing it, but it's beyond the current storytelling abilities of the industry (in that I don't trust the writers of today to create it). The only way for this to work is to control a different character.
On the story of Infamous 2, my opinion of it is described by my feelings in Kuo's Graveyard scene. The emotion was very much there--surprising me greatly--but the writing was really flat. That's embarassing and disappointing. There were a lot of themes to explore in this speech: the seperation of man and superman, what the designation of humanity means, what responsibility entails from all of us. Instead it was about Kuo getting violated by a machine, which doesn't go places except in the ending. However, the series is still a watermark in videogame creativity. I never expected such a view on ice powers, similar to how I never expected giant trash monsters to have great significance in a sandbox.