You have to factor in every single monster, their traits, the different skill effects (stat altering/status-inducing and things like Mean Look), stats, trainer Pokemon AI (can't have your Elite Four Psychic master attempting to use Psybeam on your Houndoom, eh?), and loads of other junk. It'll be mammoth.
Basically then, I'm of no use here , despite having been an RM2K/3 user for nearly two years now. I do know what you've got ahead of you though, and it'll be interesting to see if you can pull it off. Best of luck.
I know its hard, thats why i'd suggest starting from the basics, such as coding attack and items first, by having 1 or 2 pokemons as test subjects (>=D) and then try to AI them and see how it works, well thats just a thought