I modeled a tree not long ago and I had the same problem as you do.
This is caused because ZSpheres have 8 divisions along their diameter no matter how big or small they are - so basically your stump has as many divisions along it’s diameter as the tiny branches do.
One thing you could do is go out of ZBrush to a polygonal modeling kit like Maya or Max or XSI, and maybe build the base mesh there. You could also import a ZSphere base mesh with only the larger parts (stump, main branches), and use extruding in maya/max/xsi to make the smaller ones. This should work, but it requires more software.
If you want to resolve this in ZBrush, what I recommend is using Remesh.
You can use Remesh on your existing tree, with all the details, and then project the details on the resulting mesh. You can also use unified skin instead of adaptive skin on your ZSphere model, which is what I would do, since projecting so much detail will probably just explode your mesh.
This is how I resolved the issue with my tree (unified skin, and then add detail). But keep in mind that in case you ever want to animate it, it won’t work. For that you’ll have to make a proper basemesh. A unified skin is a great mesh to sculpt on, but nothing else.
Hope this helps you in any way. Good luck!