The metal tiles are perfectly square, as though they are being seen from a top-down perspective, while everything else is seen from a more slanted view. I think that you should begin by fixing this.
There is no consistency between the shading and outlines between the different parts of this image. This should be one of the first things that you fix because the more detail you put into something, the harder it is to change its basic style. I'm going to guess from the image and the comments that you have a habit of learning how do draw different things from different sources and then emulating their styles on those objects. Learning from example is good, but you have to put your own twist on it and form your own style to tie it all together. Don't just learn how to draw a particular object, learn why the artists have drawn them that way and try to apply these rules to other things.
The branches on the tree in the foreground look slippery, more like squid tentacles, due to the smoothness and the way that you've highlighted them.
I really like the flowers on the other tree, but while you've outlined the flowers themselves, the internal features such as the stamen are almost unreadable because they are not outlined.
I sort of like the gradients and think that they are appropriate in this case, but you should be prepared to receive a few negative comments on them since they don't fall within the boundaries of traditional pixel art. The same goes for anything with transparency, such as the beams of light under those glass platforms leading up to the edge.