I made an edit to address certain points of your tree:
(1. and 2.) As I mentioned before, the perspective of your original was misleading. Your original tree appeared to be in two perspectives: if you cover up just the leafy portion, it looks as though we are above the tree, but if you cover up the grass, it looks as though the tree is growing over our heads. As you can see in number 1, I edited your original tree to show the whole tree as viewed from underneath. I left the leaves the way they were, but I put the lower half in the same perspective as the top half--now it looks as if the tree were floating in the air on a square patch of grass, and we were looking up at it. You can see how now we can see everything from underneath.
But in isometric perspective, everything that rests on the isometric plane should have the impression that it is being viewed from above. So in number 2 I put everything in an overhead isometric perspective. If we are floating above the tree, then our view of the upper trunk should be blocked by a portion of the leaves. So I edited the leaves to cover up more of the trunk.
(3.) I also noticed that the leaves were amassed into a single huge blob. But if you think about trees, because every leaf is attached to a branch, the shape of the leaves is directed by the shape of the branches. (You can see this in the reference pictures of trees that Malor posted). Leaves don't just grow anywhere--they have to be attached to a branch. So I drew in some lines that divided the blob of leaves into smaller sections that would follow the shape of branches beneath them.
(4.) I think the gaps you had in your first tree were a good idea because they added interest and made the leaves less of a single blob. But the gaps you put in were weird because they allowed you to see through the entire tree at the very center of the leaf mass--the point where there usually are the most leaves. I put many small gaps around the edges of the leaf mass. It is easier to see through the edges because they are less dense than the rest of the leaf mass. I also made some larger gaps near the trunk. This is because the larger branches of a tree generally have less leaves than the smaller branches. The heirarchy of branches goes like this: trunk->larger branches->smaller branches->twigs->leaves, so you can see why there would be less leaves growing close to the trunk and large branches.
(5.) I removed the black outlines, because black is a color that in real life only occurs in areas of very deep shadow. I replaced these outlines with the dark brown that was used in the tree trunk. I also used a dark purple to indicate areas of shadow. (A lot of shadows in the outdoors have a bluish tinge--this is because even though the shadow isn't being lit by the sun, it is still being lit by the ambient light of the blue sky). I also edited the base of the trunk to look more like the base of a cylinder in perspective. In my opinion, helps root the tree into the ground.
I learned a lot from editing your tree, and I hope you do too.