32 legendaries? That's a hell of a lot :\
Also, I think you're rushing things a bit. 300 new Pokémon aren't going to come out very well unless you put a lot of time into them. Some of them seem a bit iffy even now; for example, I can't really imagine a cymbal or a clock working as a Pokémon. Go ahead and prove me wrong, though.
You seem to be rushing your sprites, too. 5 minutes for a sprite is nothing; when I sprite, it takes me around an hour to make a medium-sized Pokémon sprite. Even the smallest sprites still take me at least 30 minutes... Trust me, you do not want to end up showcasing your game with rushed sprites.
Now for the story. The basic plot sounds good so far, if a bit far-fetched. However, this is a game, so do what you want ;)
Does the player have to play as a boy? What if a girl wants to play this game? It wouldn't feel right to have a girlfriend in-game if you're a heterosexual girl IRL...
And where do Charon, Looker, and Sinnoh in general come into your plot? If your game and the main story is set in a new region, why does the player have to go to Sinnoh and repeat exactly what happened in Platinum?
Finally, story and MMORPGs don't generally go well together. It's hard to include a good story when you have dozens of other people rushing around your maps. MMORPGs tend to focus more on exploration rather than story, anyway.
Anyway, have you started actually making this? Which program/language are you using or planning to use? Your features are pretty ambitious. If you're making an MMORPG, you'll want to store all the player information on the server, so people can't cheat as easily. Storing 3000 Pokémon per player will use up quite a lot of memory.
Am I the only person who gets the feeling that this isn't actually going to be made, and is just a very ambitious dream? If you're making a game, you have to be realistic; although you might want your game to have hundreds of new Pokémon, all the regions, and be an MMORPG, do you have the skills to actually make a game with all those features? You can't just hope to get other people to design, sprite, and code everything for you - you have to do a lot of it yourself. Nobody will want to work for such an ambitious project unless they can see that you're committed to it.