Emulator

Currently, any Wii Remotes set as "emulated" in the "Controller Settings" menu will be automatically connected when booting a game, which can cause problems if you regularly switch between solo and multiplayer, or play games that only allow two players (like Skylanders).
Additionally, the "Connect Wii Remote X" hotkey actually disconnects the specified remote if it is set to "emulated", and can't connect the specified remote if it is set to "none", and manually switching a second Wii remote to "none" while playing, instead of disconnecting it via the hotkey, causes issues.

Take Kirby's Return to Dreamland as an example; In that game, when all 4 remotes are set to "emulated", all 4 player icons appear at the bottom of the screen, even if you only plan to play solo, and fixing this requires you to tab out and adjust the controller settings, or make a hotkey on controller 1 to disconnect other controllers every time you boot up a game.

A solution to both of these problems would be to add a toggle next to the Wiimotes in Controller Settings (like the sideways toggle in Wiimote configuration) to have that controller slot not automatically connect on boot (something like, "Disconnected by Default"), and instead require the use of the hotkey to be connected, but still allow the emulator to register it as a controller slot that exists.
So, depending on your setup, you can set the default behaviour to be that only controller 1 is connected at all times, and then when someone wants to drop in, they turn on their controller, press the hotkey to connect, and they get added to the game (as an example).

Considering using real Wiimotes already has automatic scanning implemented, and that being more difficult to do for generic bluetooth devices, this seems like a nice middleground solution.