Hi,
Here are some suggestions that I have for Zbrush, not sure if they have been raised before or if there is another way to go over them. I’ll try to keep this post up to date.
Subtools Folders
I would look at the way Photoshop does folders and layers and try to do it the same way. Another option is Maya Outliner and the way you can create groups.
Material Shaders
Being able to see specular, diffuse and normal map in the mesh. I love the idea of painting directly in the model all the maps I need including specularity but since I cannot see it in realtime I end up going to other applications.
Spotlight or Paint to Texture
A bit like the newly released Mari. I’ve found that sometimes I have to subdivide like crazy just to work on polypaint without actually adding new details to the mesh itself. If I could paint into a texture I would be “free” from these issues and use Zbrush more to even fix texture seams.
Create Holes in Meshes.
I know we have the amazing Zspheres2 and topology tools and Shadowbox but if for example Im doing longhair for a character and want to actually separate strands and make holes its a pain to use Goz, make hte holes and come back, I wish I could just delete a part…somehow, I know you guys will figure this out 
Small workflow tweaks.
- Being able to mask quickly by polygroups without having to go into Move/Scale/Rotate mode and do the selection and then coming back.
“Mask by Polygroups” with an added On/Off button
Easier way to manage new materials and Matcaps, the import function where it replaces them its not smooth enough
And finally just better documentation. I know you guys work hard on this but I feel the Wiki really hard to use since the search doesnt work that well and there is a lot of out-of-date information.
3Ds max has an amazing documentation that allows me to explore areas of the UI I never used before and in Zbrush I find myself stumbling on amazing features or just reading them by random in the forums…
EDIT - just removed the importing OBJ since Noobve just showed me a easier way.
