I don't like the map, I would actually prefer it to be empty rather than overstuffed as it is now. There's really little reasoning to how you're using your upper tiles, you're just putting on every single one of them in your map somewhere. This is not a desert, there shouldn't be a cactus on that hill when it's surrounded by a whole bunch of grass, flowers and trees.
Second, the hero can't go anywhere. Every area is blocked by a huge amount of upper tiles. The map leads nowhere.
The left side of the map has a hill going up, yet it's not mimicked in the right side, but the bridge still leads to it as if they were the same elevation. As Serenade said there's no need to have the waterfall there.
I think studying SNES maps or other commercial 2D games would be more helpful. I think Seiken Densetsu 3 in particular had very good mapping.
http://mmxz.zophar.net/rpg/mana2/images/images.html
Take a look at them. They don't use very many upper layer tiles. The ones they do use, they don't overdo them, but use them in a way that makes the map look good and function well.
I would limit the amount of upper layer tiles you use to a few flowers. Try to make the maps so that the upper tiles can serve as landmarks.
Here's an example: One map would have mainly white flowers and large grass. The second map has a wide river and some yellow flowers. The third map has broken down pillars and rocks where the ruins used to be. The fourth map is enclosed with trees and mushrooms that leads up to a cave entrance. That would be better upper tile usage, as it could help guide the player, differentiate the maps to provide variety, and sometimes even tell a little backstory to the area.