Wow, even better news. I wanted to be able to manipulate the GPU clock speed as well, found an app that works for any ICS/JB phone (called Faux123, requires root, unfortunately $5 on the play store). It allowed me to set the CPU to performance max (again 1890 MHz) and also the GPU to performance max (for the S4 it's 450 MHz, I believe for the HTC One it's 400 MHz).
Ran Mupen again (stock one from the play store) and performance was great. Super Smash Brothers ran completely smoothly at 45-60 FPS during gameplay. I am almost completely certain at this point it is a CPU/GPU throttling issue. I'm honestly not sure if there's any way to force higher clock speeds without root.. can try to look into it online but I'm not strong with coding or anything like that.
Let me know if you'd like any test reports or anything while running the app with the higher clocks, thanks!