I have, it's not.
The problem with current P64 input plugins is that they don't have any kind of automated way of telling if the controller is connected or not. The settings have individual tickboxes for them. Mupen64Plus ignores a controller if it's not connected but then autoconfigs it if it is. For instance, I use four wireless 360 controllers on my machine. If I turn only one of them on, Mupen64Plus has only one controller in the game. If I turn on three and restart it, it has three.
In P64, If I configure four controllers as connected, they all work just fine. But then if I turn off three of them and restart the emulator, P64 thinks that I still have all four connected. Since they're all set to use a "Wireless Xbox Controller For Windows," the one controller that remains connected now controls them all. I'm having a hard time finding an acceptable workaround that doesn't involve me checking and unchecking settings every time I want to play.