Okay I've been out of Rom hacking for years now but here is something i think is still the same.
You can't add more pokemon than are in the game.
For example, if you want shadow, pure, galaxy types of a pokemon, you will have to replace current pokemon with the texture edit/ stat edit/ type edit/ Pokedex discription.
So lets say you have A Normal Charmander, Galaxy Charmander, Shadow Charmander, and Pure Charmander. You will have to get rid of 3 other Pokemon. Right?
For one I don't know how good the tools for editing 3ds pokemon games are. I've been away from it.
The randomizes encounters also. You will have to find a way to change encounter code for the game. Last time I checked, You can change what Pokemon are encountered in each area, but not possible to encounter just any pokemon because each place had a certain allotment. If there is a route only 1 Enounter type and it's Zigzagoon, You will have to remove Zigzagoon and put another Pokemon, like Torchic. But you can't add another encounter like Ralts and Torchic, just Torchic.
I'm going off what i know about GBA Hacking.