It is recommended you use a Mayflash branded GameCube controller adapter with RetroArch as it has a switch allowing you to select ‘X-Input mode which works natively in RetroArch. RetroArch GameCube FAQs Does A GameCube Controller Adapter Work With RetroArch? So experiment and see what works best with your system. There are stacks of other options here too (which are fully detailed in the RetroArch Dolphin Core Options documentation. I recommend just upping to a resolution until you either get to you the maximum your display can handle or whatever the device you are using can handle before the game framerate begins to slow down. Simply select ‘Internal Resolution’, then choose the resolution you require.
Dolphin Core Options – Upscaling Resolution