As far as the flexibility thing goes, I also would love to see some more of it, but it wasn't totally intentional in RBY from what I understood. You could fight Sabrina or Koga in whichever order you really wanted, I guess you could count Blaine in there if you fought Koga before Sabrina and just Surfed to Cinnabar instead of going back to Saffron, but it didn't scale the levels accordingly, it just let you do whatever. But for like 3-4 gyms it definitely would be cool to be let the player do the gyms in whatever order they wanted, and had different flags set up for scripting that allowed the story to progress in whatever city it needed to.
I could definitely see using the Gyroscrope for puzzles in the gyms though. Maybe have to move something into the proper place using the gyroscope, and then one it was placed it could let a gate up or something? I could see this working in a Rock gym, rolling boulders around.