Since a lot of packages required for unity conflict with the stock packages, it might make sense to change the prefix for all unity specific packages to /opt/unity - that way both the stock as well ubuntu specific packages can co-exist. This would especially be useful in the longer run as Ubuntu is diverging away from mainstream gnome. For eg there's not going to be a gtk update for the next version of Ubuntu and so on.
This is more an attempt to brainstorm rather than file a bug (Github we need forums!). I would be more than glad to pick up the task of updating the PKGBUILDs to use an alternative installation path.
I agree that we will need to do something eventually. Here's what I think about our possibilities
Install to /opt/unity
If we choose to go this route, we will need to maintain quite a few GNOME 3.4/3.6 packages (installed also to /opt/unity) since packages, such as gnome-settings-daemon will probably stop working with GNOME 3.8.
Rename the libraries
This is similar to what Linux Mint does with their forks of GNOME packages. This would be cleaner (with regards to installation prefix, etc) and wouldn't require hacks or launcher scripts as we would for installing to /opt/unity. We would still need to maintain GNOME 3.4/3.6 packages though + we would have the extra work of making sure that the renamed libraries work properly.
Port the patches to GNOME 3.8/systemd/etc
I think this is the best idea in the long run. I've already done this for gnome-settings-daemon, gnome-control-center, and indicator-datetime for the GNOME 3.6 release cycle. Ubuntu's patches aren't too complicated and this should be pretty doable. This would still require the stock packages to be replaced.
EDIT: There's also a fourth possibility I was considering earlier: (EDIT 2: Why won't github make that a 4...)
One thing I know for sure is that I'm definitely not going to have some weird combination of GNOME 3.0/3.4/3.6/3.8 :D
Hopefully, things will get better for the Ubuntu 13.10 release cycle. GNOME 3.8 is dropping the fallback session and its libraries, so Ubuntu will either need to maintain dead code or write replacements for the dropped libraries.