Normally, my answer to this would be to update to the newest development version, enable the Hyrule Field Speed Hack in the game properties, and change DSP emulation to HLE if you aren't using HLE already. But since you have OS X with Intel HD, updating beyond 4.0.2 will probably lead to major graphical problems with things like water. Give it a try if you want to, and go back to the older version if the new one has too many problems.
By "runs other games well", do you mean PC games or emulated games? It's common to be able to run PC games well but not PS2/GC/Wii games, because of the extra power needed for emulation.
By "runs other games well", do you mean PC games or emulated games? It's common to be able to run PC games well but not PS2/GC/Wii games, because of the extra power needed for emulation.