There is something that I was thinking about from the very beginning. I'm not sure if this comes from lack of experience or if it is just a bad habit.
Please look at this:
I marked you some spots (the most obvious) of your image that have no form at all. Your sprite is very detailed and I'm a big fan of your endurance, but when you leave this parts as they are, it's no wonder that your tree looks flat.
Normaly, you do pixel art step by step. Having a base, adding a shade, adding a second shade, adding higlights, and so on. I think you missed these spots while stepping forward. Since they are everywhere they are really disillusioning.
- Make sure to give everything a form, even when it's further away. And cut out things you don't need. There are no such things as round blotches of green on a tree.
- Use your colours. Your darkest shade is only presented in such a small area. Why?
- Clean out the edge of your sprite. (This is maybe the easiest way to take your tree onto the next level.) Make sure it looks complete, as you did in the lower left corner of your foliage. And you don't need outlines in such a realistic sprite. They are disillusioning as well.
Once again, I want to encourage you to take everything step by step. Especially for training. Don't miss spots, take your time to finish things before you start with others. Take time to think and look. You have the endurance to do so. Use it in the right way.
I look forward to see more of your art.