Still don't get what the issue is. dpkg --instdir will put stuff whereever you want it (but then it's your problem if a system service doesn't find it or a part of it, obviously)

Again, it seems that you aversion stems from how you use your apps - the convention of putting all executables in bin is because that's what's in path and that's what you'll see when you use it from a command line. When you click around, a graphical (hierarchical) layout is preferred, and most desktop environments do just that - they put stuff in /bin to keep compatibility and put shortcuts/link into the menu entries - everybody happy.

FWIW MeeGo uses something very similar in layout to what you propose so looks a lot less like a traditional linux (it puts the apps into their respective /opt/namespace/... so nobody touches /usr/bin et al)