There's a newer version of Morphgear available, maybe try that one. Not that it will make a huge difference, but it's worth a shot.

Also, don't forget you can toggle autoframeskip, adjust sound quality and so forth. I found I am better off with high quality sound than low, when it comes to emulation speed and so forth.
As well, you can also try the older PocketSNES BE. Many people rave about how MorphGear is much better than it. But to be honest, on my particular PPC, 16-bit high quality audio plays much better in PocketSNES than Morphgear. And Final Fantasy III US plays much better for me in PocketSNES.
It's all debatable but keep your options open anyway.

JJB