I think I figured out why most of the stuff hidden behind C6 was deemed to be endgame only in my design doc; It's because you can't go back to most of these places at the moment. Since you get warped to later stages by defeating bosses and collecting infopacks, you can't just waltz back a stage behind at-will. I'm seeing on my map that there will soon be a spot where you can explore a little more, but as always, actual design trumps over what I've wrote 'ages ago' in a doc.
I've also decided to remove the 'Ultimate Teamwork' skill and instead upgrade the 'Teamwork' skill by itself. The reason why there were two was because I didn't know at first that you would have many skill levels with different effects. I've thought about what the new skill would be, for a little while I thought that it could be a turret, but that looks a bit too much like the 'Admiral Stand' skill. So I've came up with something called 'Gun Roulette'
Time spent on the project so far: 446 hours
Currently working on: Moving on with the story