Another glitch that I am not sure has been reported before.
Anyway, on another note since I just beat the main storyline there was a few opinions I had.
I was disappointed by how the Four Horsemen just sort of disappear mid-way through the story and are never talked about again save for once or twice.
Difficulty seemed a little erratic at times going from easy to hard. Mostly because of so many heal points throughout the game. I wouldn't have minded a few spots in the game that acted like gauntlets besides the Elite 4.
I disliked the player character's dialogue at times. But that is a purely personal opinion. I am sure everyone has different opinions about the player character's dialogue.
Besides that I had quite a bit of fun solving your puzzles and getting your references. Though I mostly lucked out on your mazes and puzzles. Took a good 30 minutes or so to beat the boardroom, had a chikuwa from that thing near the monks and bought everything the chef had just in case I needed any of them down the road, knew I needed a Magnemite for the elevator, but happened to catch a Ditto before getting to the warp pad, got lucky in the madio cave, and got even luckier in the super trick room, but all in all had fun with them. You did trick me once though, when I returned to the Island of Calm to get Chikorita and remembered seeing a Phanpy on one of the spawn tiles which I didn't catch at the time, and then I remembered Shadowu (spelling that wrong I know) and thought I would catch him only to find he didn't spawn anymore. Got a "Aw, darn it." outta me when it happened.
Speaking of which, besides Phanpy do any other hidden Pokemon spawn on those tiles? A simple yes or no will work since I would rather search all the tiles knowing I am going to find something instead of searching all of them and not finding something.