My opinions of the idea above.
1.) There are a lack of Pokemon RPG's which you may play as a legendary. While this does drastically decrease the posibilities of Pokemon to choose from, it would make an interesting, and refreshing change of pace for an RPG.
2.) Crossovers. In my opinion, they don't work. Many ideas and rules from one story combined with the other can result in a far too complicated, and often contradictive Role-play, which many would find difficult to follow effectively.
3. Erm... Insert a criticism of your choice.
All in all, it could make for an interesting RPG, but the fact that it would be a cross-over Role-play would reduce my likeliness of joining said game. While my report of your idea may be short, and possibly of little help, I just thought I'd voice my opinions here.