Okay, now firstly..
To be honest the region name (This might just be me) but Core?
It needs to sound more exotic and real, I think I'm just being to picky on that one lol..
I like that your adding new music, its a good feature, but i think u should stick to just using Pokemon music, not Zelda.
I agree with what alot of other people have said about using Mario, Luigi, so on..
They don't belong in Pokemon games, If I wanted to see Mario I would play Super Mario Bro's lol.
I'll be intrested to see how you insert those new moves and how they turn out
Your maps...
I don't need to say a thing as Swiftsign has beat me to it.
Maybe use the D/P garchomp back sprite, as the mouth does look funny and its made like that coz B/W has different frames.
I like that you gave Vulpix/Poliwag there DW abilities, nice idea.
I think the Rivals dragons should be caught, but maybe near the end of the game.
In the screen with speech, it should be like this..
*DR GIRL: I wonder what I'll do today...
(Next Line)That dream last night
The best friend rival looks bad, you choose some messed up colours..
Purple and Yellow, yuk..
Also maybe make a whole new person instead of just editing emeralds sprites?
Sorry, I could keep going but I have to leave lol..
*ON another note, I will make a few maps for you if you would like maybe only one or two, but they will be very good quality? I'm extremely busy with my hack otherwise I would help you more, I think people need to take it easy as I know how hard we all can take criticism sometimes. Pm me and let me know 
if not then good luck!