Clouds in the foreground look very weird (they look very small and opaque).
Yup.
Unless the clouds are actually about the size of the sprites there, that would be impossible from this perspective, seeing as the characters would be behind the clouds. They do look very nice in the background though. On top of them not working out perspective-wise, they also serve to clutter the foreground a great deal.
Although I think the clouds in the back look very beautiful the way they are now, I can't help but feel the background is also a bit plain. This is not a bad thing really from a gameplay perspective, but I don't think it would hurt to add a little more. I think a nice idea would be to add some other islands in the back as well, behind/within the clouds. (If that makes sense in your game's world.)
As for color, I think your ground tiles (actually, most of them in general) are quite contrasty, and should be toned down a little, maybe. Your characters might get lost.
And consider adding some extra transition tiles in the ground over the sides, such as from the grass to the dirt. The change is abrupt right now. There should at least be a shadow there, I think. (And if you're going in the route of removing the foreground clouds, some extra detail tiles to make that area underneath the actual walkable area look somewhat interesting - but not distracting.)
