Wait for PPC2k3 and an Xscale version of PocketSNES
Although you could also try overclocking, if you have a PXA255 setting the memory up to 118mhz has some major improvements.
If you don't want to go that route though and you are using Bleeding Edge Pocket SNES, go to Options ---> System and set cycles to 1000. (YOu have to manually enter the number in with the virtual keyboard). Turn Show framrate off. Next go to display and turn off transparency effets and auto frame skip. Not put your frameskip to 3 or 2. This alteration works on a lot of games such as Super Mario World, FFIV, Zelda etc. (for some of these though you may have to turn transparency effects back on)