Sure, no problem at all. Goodluck though, you're gonna have to redo every Pokemon's moves from start to finish lol. It's a pretty long concept and deciding when a specific Pokemon can learn a specific move.
I don't think there's a way to do that without mastering some ASM code. I replace the older Pokemon with the new ones but I also use the 17-18 empty spots where you can insert Pokemon. If you open up any program that shows the Pokemon, you'll see there's a lot of empty spaces you can use, but those specific spots can't have icons nor can they have their pokedex information edited.