Puzzle ideas?
Jumping puzzles with moving platforms would be nice. There are already platforms that will appear and disappear. A really cool thing they could do is a jumping puzzle that takes place on a living creature like in Shadow of the Colossus.
If it was up to me, I would not have any jumping puzzles in game at all. I never liked Metroid, and I dispised Mario Brothers. But a lot of people like them. So they can stay.