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Just so everyone knows before reading this, I don't have much knowledge of hex, and some things I'm suggesting might be impossible.
1) With the two spaces at the end of the dex that don't crash the game (252 and 254, if I remember right) insert custom front, and if necessary back, sprites for the Custom Sprite Pokemon on AgiXP.
2) Go on the Hex Editor. This is where my lack of knowledge on Hex kicks in. You need to add some kind of coding to add to the typical standing Pokemon script so that that particular Pokemon will always call to the sprite/sprites you inserted through AgiXP instead of the normal sprites, which will still load for every other member of that species. If you pull this off, the Pokemon will be identical to the rest of its species in name, moveset, stats and everything else. Pokemon bred by this one will not have custom sprites, and upon evolution the Pokemon will have its normal sprite.
This is great for making special Pokemon appear in game, such as Fossil Aerodactyl or something. This makes it so that you don't have to make every Pokemon have a custom sprite, and it can also be fun to just get a devamped sprite from a later generation rather than the same old sprite for everything else of the species.
I'm not sure what the code to add to the standing Pokemon will be. If anyone can figure it out, please post here after testing so others can use it, too! I'd gladly give credit and add it to the first post, if you're okay with that.
I haven't been on this site for a very long time. Sorry about that! >.<
I am probably not going to get very far in the ROM projects that I've started, at least until I get more experience hacking, so I apologize.