Emulating a gamesconsole based on a microcontroller is surprisingly hard for a normal computer. Other than the actual clockspeed, PCs are faster because they have lots of hardware specifically for doing certain tasks like rendering video and playing audio.
In the case of audio, the CPU gives your soundcard 4kbytes of data at once, then forgets about it until its time to get another chunk.
The Pokitto, on the other hand, outputs sound one bit at a time. The emulator receives that data bit-by-bit and has to try to assemble a buffer that your soundcard can be happy with.
If the bits don’t arrive fast enough, you get a skip.
In the mean time, your videocard is just sitting there, thinking why’s the CPU doing my job? Same situation: 619520 bits of image data, every frame, and the emulator can’t use the PC’s extra hardware at all.
Since all the emulator sees is bits coming in, its impossible to do things like frameskip and it wouldn’t help much anyway.