I have this idea of having multiple scenarios that would follow three different groups of people. The main, main protagonist would have the power of Sora from Kingdom Hearts, but his personality would be more 'modernized'. I'm still not sure about whose power his best friend would have(Riku maybe?). They would be the main protagonists of one scenario.
The other scenario would follow two other people,who seem to have their power longer that anyone else. So long, that they have multiple powers. One would have the powers of Byakuya, Renji, and Ichigo from Bleach, while the other has the powers of Neji and Sasuke from Naruto.They have some knowledge of how everyone got their powers but are unclear of certain things themselves. They act as peace keepers but only when situations get too out of hand.
The other (last?) scenario would follow a single boy whose power was everyone's in Organization XIII . He has everyone's power due to a slight mental disorder which results in multiple personalities. He is a rogue and watches events as they go by and only gets involved in situations that could prove beneficial to him.
The scenarios will intertwine at times, but each plays key roles in a bigger event. While trying to find the source or the truth of the obtainment of their powers, they will journey to different areas(worlds?) that whole communities have gotten powers of whole shows/games that the protagonists visit to help prevent interventions from enemies that come from different shows/games. For example One group of protagonists will go to an area(world?) of Code Geass, where Nightmares are roaming around, while another visits an area of The Melancholy of Haruhi Suzumiya or FLCL and end up getting caught up in the events without meaning to.