I was thinking about E-mouse's suggestion for multiple storylines, which would give more room to add more characters into the story.
So here's a suggestion. The current storyline can be the 'CPMC route' of the game. There can be two other routes, the UGW and MotK routes.
So after defeating Nwbi, the player is given 3 choices (much like the end of IN). They can either rush into CPMC, wait a bit, or go elsewhere. Rushing into CPMC activates the CPMC route. Waiting a bit activates the UGW rote. Go elsewhere activates the MotK route.
Suggestions for story:
Indefinite Intentions of UGW Route - The player waits a bit before rushing into the thick of things. However, in the mean time, Theorin's plans somehow fail, leading to the ruin of CPMC. Taking advantage of the power vacuum left behind, the flying city UGW, lead by the mafia, moves in to take over CPMC and the remnants of project idiot.
Embarassing Embodiment of MotK Route - Theorin's plan succeeds. CPMC sucks in all the intelligence in MotK, leaving behind a huge wasteland of idiocy in its wake. Rin Satsuki, having taken in all of MotK's essence, becomes the embodiment of MotK itself, MotK-tan.
Suggestions for bosses for the:
MotK Route - E-mouse (The one who dwells within), Donut (The Last Cream Filling), TranceHime (Puppet Dancing on Threads of Fate), Kilga, Edible, Letty, MotK-Tan
UGW Route - Xan (Incongruous Capricious Maid), Totaku/Ramus (Perilous Precarious Dungeoneer), Pesco (The Godmother of Mafia Black), Purvis (Paranoia of the Barren Path)
If you go with this, it might need a bit more work. I'm terribly exhausted from college today so if you want to pursue this then I can probably add more tomorrow.