A true Pokemon CBS is one hefty task to undertake. I can't even get a basic side-view battle system up and working without smashing my tea mug through the computer monitor.
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.