It's the same plot as long as I don't do Touhoumon Another World. And same with Geography. If I do World Link, then It'll have Hoenn, Kanto and Johto(not counting the other added region which I think is optional). Or I can do Touhoumon Emerald or Firered, with no changes except the Touhoumon.
The Touhoumon have completely different stats and movesets, and the difficulty of Touhoumon is much higher than in Pokemon. But that's mostly the only change. Meaning, it isn't just a sprite change, but it is basically the same as Pokemon.
EDIT: If you need screenshots, I can provide you with some. Like of a Pokemon, or Touhoumon, or Boneka, or whatvever. (In Touhoumon, they call them Boneka rather than pokemon)