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The buildings appear to be in a different projection than the trees, shrubs, flowers, and rocks. We appear to be seeing a lot of the tops of the buildings, but almost exclusively the fronts of the latter.
In addition, the buildings have a fairly detailed, realistic look, while the shrubs are green blobs. They don't seem to belong together.
I can't tell what the ground tiles are meant to be. Single pixels aren't very descriptive. Is it sand with tiny bits of grass? I feel like something more solid-coloured would probably work better, and avoid those awkward halos of emptiness around objects. In addition, the ground tiles currently have fairly obvious tiling, which should be easier to avoid using sparsely interrupted solid areas compared to having an arrangement of single pixels.
The lines on the roof are a bit too intense, they're distracting. I think the detail level on them should be less dense. In addition, I can't actually tell what the lines are meant to represent, so those tiles probably need a rework anyway. One specific change I'd recommend is making them slope 45, so you can make the roof rise as much as you want*, and so that it doesn't look like you cut it off mid-tile:
(This edit only has the 45 degree angles, it does nothing to remedy the density of the details.)
* To make the roof heights variable, you shouldn't have that variability in distance between the lines/details, it should be about the same.
