>>43255184That's not entirely true, at least during the GSC period. For example, Lugia was created specifically for the second movie because of the delay with Gold and Silver. The only major Pokemon left to write a movie about were the legendary birds, but the staff wasn't entirely sure what to do with them. They spoke about possibly using Ho-oh, but the anime staff heard rumors that 'Ho-oh is going to probably appear in the next game' but GameFreak wouldn't clarify anything - So they asked GameFreak to create a Pokemon specifically for the movie, which ended up being Lugia.
Similar events occurred with the third movie; during it's pre-production, the anime staff still weren't given a full list of Johto Pokemon or even the entire game's plots. The anime staff asked if Game Freak could produce another Pokemon specifically for the movie, but Game Freak refused this time, also refusing to send them any information about new Pokemon the anime staff didn't already have available. That's why the original T-Rex movie script for the third movie even came to be. After that's script's rejection though, upper management got worried, and the anime staff finally faxed over 4 designs later in the week, with minimal information about them, with the staff ultimately choosing Entei and the Unown; that's also why they're are almost entirely unrelated to their in-game counterparts.
No idea how the anime is produced now; especially since TPCI forces the staff to hold their tongues now with a lot of production information.