I am having issues with the performance of some of the more demanding games, in particular Star Fox. I am getting quite a lot of sound distortion and frame skipping. I have tried switching emulators and also recompiled from binaries but no joy. I know the Pi2 is at optimum configuration as N64 ROMS and PSX are running fine.
You could try sudo rpi-update to upgrade your firmware to the bleeding edge. I have found that this improves performance in 3D intensive games (though be aware that the firmware is beta and may have other issues – take backups!).
I found, after a recommendation from another member, that if you change the emulator used by pressing x or m at start up, it can have a huge difference in performance compared to the default for that one rom.