Again, no PS2 emulator will run well on the Shield Portable period. There's no other one you can try, nothing will work better. It's purely a hardware issue, the Shield Portable doesn't have the power to emulate the PS2 let alone Gamecube.
Nightlies are like auto-builds of the latest version of something that feature the most up-to-date changes. Just download the top version of Mupen64Plus AE from here:
http://www.paulscode.com/auto-builds/
As for what else can run, pretty much everything from PS1 gen and lower along with DS and PSP games and there's a Dreamcast emulator that works ok-ish. This includes NES, SNES, GB/GBC, GBA, DS, PS1, PSP, Genesis/Mega Drive, Dreamcast games run ok (from Reicast), Neo-Geo and some DOS games can run ok with DOSBox.