I been reading through this whole thread, and I'm quite impressed with the progress.
If you want story with plot twist and intense scenes, I might be able to help in that department.
Here are some Game play idea's:
*While progresses in the game, have branching paths that leads to different Mid bosses and or end bosses?
*Every stage has 2 different paths that leads to a so called "Alternate" stage "X" (like in Castlevania rondo of blood)
How about a "What If" mode? You play as Guyot trying to retrieve a G-unit?
Have collectibles in stages hidden, to unlock characters and gallery stuff.
I believe that will increase the replay value, hope this helps you make this game happen.