This looks absolutely fantastic! The music is great, the title theme sounds like a mix of Final Fantasy and Pokemon which is gorgeous. The maps are very colourful and detailed. Also, I like how the bushes shake in the background when you're in a battle, simple stuff like that make an excellent game.
Not sure if anyone mentioned this yet: a little suggestion, make Pokemon variants! That would be awesome, an old game that was being created called 'Pokemon: The Lost World' had very unique variations and it was very popular, unfortunately the creator lost all his files.
Anyway, Pokemon that lives at the beach may have a darker shade of skin due to constantly being in the sun. Pokemon living in snowy areas may have white fur instead of their normal fur, to help camouflage. I can always help with the recolouring but I see you already have many pixel artists prepared to do so. Anyway, that's just my suggestions. Keep up the terrific work and I will wait to see some more awesome updates!
Link to some variants made by Captain Arcane : http://www.pokecommunity.com/showpost.php?p=3069756&postcount=211