The loader has no effect on the controller compatibility.
It launches the game, then the game initialize the input (controllers, wiimotes, etc.), if it's a wii game there's nothing the loader can do.
unless you use a wireless controller, I think you need to plug it before launching the loader.
The thing is when I use the original Brawl disc, the GC controller works fine but after installing it to my HDD (using CleanRip and Wii Backup Manager) and loading it, the controller doesn't work even when plugged in beforehand. Any idea what could cause this?