Yeah, it makes sense. In fact, the hack I'm working on right now has different biomes...
Anyhow, what I'm saying is that the tiles' styles are what don't match. On one side you have B/W trees and a gate from Unova and on the other you have FR/Lg grass and flowers. It's just graphically unappealing in some sections, if you understand this.
The best thing anyone can do in a hack is evening everything out to one style, which is difficult, especially if one isn't good at making tiles. Experimentation takes forever, but it's by far the best option. Patience is key.
EDIT: Also, if you haven't noticed, palettes 9-12 change from map to map, allowing for incredibly broad palettes for different areas. Just though I would let you know, since a lot of the palette 12's aren't used in the ROM and you seem to be space challenged.