Being honest, the graphics and the mapping in this game are some of the worst I've seen in a fan game, and that's simply a criticism. The sprites that you commissioned, such as the overworlds and trainer sprites are great. But the thing is, everything you've commissioned is far better than everything you've done. The graphics you did yourself for the battle system and the intro don't suit a Pokemon game at all. You're mixing pixel art with graphic design which does not work. It is a clash of style. The fogs are way too heavy and make the clarity of the game fall to zero. They're simply hiding the fact that there is terrible maps underneath. The maps I've seen on DA are open, messy, the paths don't work with the ground, empty, shapeless, and the pink trees and odd colours do not favour the game at all. This isn't a solid Pokemon game at all. The overworld maps and so on do not resemble a Pokemon game. It looked a lot better like this, despite being quite unoriginal it still had correct colours, and some semblance of decent mapping and clarity. I'm sorry to say, but you're not doing the game any favours with the direction you're going in with these graphics, tiles and the way you map.
The first thing I would actually suggest is that you get a tileset that works together, and don't put things like paths which go on grass onto mountains. I recommend that you go back to normal colours and avoid pink trees and brown water and so on. Then you're going to need to learn to map a lot better. Your routes are not playable. The player is simply going to walk through empty maps with open spaces and it's simply boring, as well as seeing hundreds of tile errors.
If you need help with any of these things do not be afraid to contact me. I think you need to hone your skills and find a direction. It's good to be original, but remember you're still making a Pokemon game. And you still need to worry about clarity and making the game playable.