VBA is the best and most popular Gameboy Advance emulator around. Emulates GBA, GBC, SGB, GBA roms! Supports ZIP-ed roms, so that after downloading files from the net you don't even have to un-zip them
I don't have a wii u anymore to test it myself, but if homebrews are not visible on the wii u menu I think you can press L + R + minus to open the plugin menu, there should be an option called "homebrews on wii u menu" or something similar
Or when your player dies, you can say in code, if enemy exists, do nothing, but if enemy does not exist, then create enemy at certain spot. (This would be a pain tho for lots of emeies)