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The square water confirms the map will be made up of tiles, correct? So what the fuck is so hard about dynamically loading and dropping tiles as you cross certain boundaries? This is how it worked in RSE, and all that happened was the game paused a few frames when you entered a new map. Given the speed of the 3DS processor, there's no reason it wouldn't work.
There's no good reason to implement gates. If they do, I'll be pissed.