I haven't messed with r200 yet, so I've only had GCN controller support to this point. I also don't use GX, but instead CFG USB Loader, so I can't say for sure how GX handles multi-disc games with Devolution. With CFG, however, I discovered that disc2 (which can have ANY name at all, only Dios Mios requires "game.iso" and "disc2.iso", which I'm pretty sure is all lowercase) has to be in the games folder and not in any sub-folder therein. So if I were you, I'd try putting disc2 in the games folder (and personally, I follow the convention of "Game_Name_Disc2.iso" so you can have several multi-disc disc2 ISOs in the folder and know what's what).
As for the Wii U Pro controller, I'm pretty sure I read that you can use it on the original Wii with Devolution.