One feature I'd love to see in the future would be to be able to fine tune where models and exports are stored. I am prone to working from multiple computers at any point in the day as inspiration hits me.
To keep my various projects in sync I use Dropbox to store my writings, clip art, and blender models. I'd love to do the same with MakeHuman.
One thing I have noticed that is a minor annoyance at best. If I hand copy a MHX file from my Windows machine (the only place I seem to get MakeHuman to work properly) and load it on another machine (Linux or Windows, architecture doesn't matter) the textures get lost. No biggie, I just go in and add them.