Anyway... I found the source of the problem. And sadly, the HTML5 version might be in jeopardy because of it.
How Game Maker HTML5 works is it stores all the game's graphics (sprites, tilesets, backgrounds, etc) into a single 2048x2048 texture.
What this essentially means is that I'm limited to 2048x2048 (or 4194304 pixels) of unique artwork. While this sounds like a lot, the Pokemon sprites and the base indoor/outdoor tilesets alone eat up 79% of this. Then there's still character sprites and artwork, miscellaneous menu art, attack animation art, and the possibility that I might need to expand on my current tilesets. Not to mention the fact that I won't be able to utilize 100% of this texture, since the artwork won't be able to be perfectly packed into this 2048x2048 texture so as to not leave small packets of unused pixels all over the place.
So basically, I'm not sure if all the game's art will be able to fit within this texture when it's finished. Currently it will though (in theory, if divided up right), and there might be the possibility of manually loading other graphics outside of this texture to allow for more artwork, so I'm not giving up on the HTML5 version just yet. Only time will tell if it'll pan out or not.