I'm having some trouble seeing all the positions, too...
But I think that's a sizing issue. When I run it in-game and zoom in a little, the sprites will be a little bigger. That, in turn, will make them much easier to see. I could, of course, put forth the effort to open them outside my browser and zoom in. But I'm lazy.
The palette idea is probably a good one. Although, now that I look at it well, the darkness of the above-ground really makes the tree and bush varieties pop. Maybe it's the ground tiles that make it difficult, more than the tone? The random rocks strewn about look great in the stone tiles (like next to the boulders!) but kind of weird in the grass.
Still, the more I look at it, the more I like it - dark and all.