At the beginning of the vid I thought of Alma... ;_;
Why are you doing this to me? QQ
But seriously: I like the idea, but wouldn't it be better to use the ghost battle? If you don't want to customize it via ASM to fit your needs, you could use JPAN's hacked engine to (some sort of) keep the ghost by changing it so you battle one of the 25 unused pokemon. Just a suggestion, though.
Oh, and: will we be able to jump over that 1-block-canyon thing seen at the end of the video? Or will we fall down? Both ways would make awesome puzzles possible easily! The other thing I can think of at the moment would be being blocked, but that'd be too easy, right?