Well I have decided I will edit the ROM itself for the most part, I got the tools I need. I already figured out how to make a wild Pokémon use hyper beam, and I have figured out how to modify the level, but what I don't know is how I can change the Pokémon's official name and how to replace the Pokémon's sprite on the battlefield. I have realized that simply putting a new sprite in to the video clip won't work since hyper beam in that generation also means blinking a bit.
I also still need help with finding someone experienced to make the sprite for me. Does anyone know where I can ask for help with that? If not I'll try making the sprite myself, which won't be easy as making sprites isn't something I'm used to doing.
I tried that link but it doesn't help much as I have no idea how to open these files. If it helps I use Windows 7.
And I want it to happen in the first wild battle, after I already beat my rival.
EDIT: It's been almost a full day and no help yet. Ah well guess I have to figure this all out on my own, won't be easy, but I can do it.