Okay, now when you say "Number of pokemon of trainer" do you mean:
1. The total number of pokemon the trainer is carrying?
2. The Pokedex numbers assigned to each pokemon the Trainer has?
Because if it's #1, then (hypothetically) you should be able to use Kazo's Trainer Editor to edit pokemon species and movesets without messing up the Wild Pokemon Editor as long as you don't increase or decrease the number of pokemon each trainer has in Kazo's editor. Right?
However, if it's #2 then I guess we're screwed until someone releases something better =/
Also, you said it's "One of the main reasons" it won't work. Are there other reasons that make my solution invalid?