Comment 9 for bug 133374

I understand that n-m 0.6.x is very limited by design: only manages one connection at the time, no support for static IP config and per-user configuration only. This is why I think it has primary use only for desktop users with simple setup, which more or less means one active connection. I think that is one of the reasons n-m makes sense on desktop only and therefore we should really think what is more likely config in such case.
I would say that your example of two interfaces that are active at boot is probably not very typical configuration - I would say typical desktop has one network interface and laptop have two, but in both cases it is one connection used at the time. So n-m assumption is not that wrong here.

There was some discussion in past to change /etc/network/interfaces config and mark n-m managed interfaces differently (not just dhcp as today) - that way we could differentiate static, dhcp and n-m interfaces. I am not sure if this would be good move, but it is worth considering. Current workaround (remove interface from config file completely to make it work with n-m) already goes in that direction.

I completely understand your pain in maintaining n-m for ubuntu: due to limitations you need to make some shortcuts that will hurt some people. You just need to choose less painful way... ;-)