I've had a shield portable for about 2 months. I'm trying to play Conker's Bad Fur Day, Banjo Kazooie and Marvel vs Capcom 2 on it. When I play the n64 games on Mupen 64 AE 3.0, it gets pretty choppy (around 40 fps) at any resolution. I would use retroarch, but when I launch the rom it gets choppy, and I can't get to the retroarch menu. I've seen both games run just fine on Shield Portable, so I know it is possible for them to run at a full 60 with no problems. As for Marvel 2, it runs pretty slow on a reicast nightly build (11-13-2014), even though I have seen it run just fine. My Shield Portable is running on android 5.1. What can I do to fix the framerate?

A vid of it running fine:

 

Muphen ae is old and buggy as hell
Reicast is in alpha stage, anyway you should try the latest version.
Retroarch cores are buggy.
When you run RA n64 you can t use the joypad, you have to go back with the touchscreen (enable the controls overlay) and then press a button.
You will see Gamepad connected.

Keep in mind that your gpu is old, it does not fully supports opengl 3, it lacks latest drivers, and android emulators are not so good.