So I have been able to get Super Smash bros. to work fine on Mupen64plus with both the 2.6 and 3.0b2 builds using the rice plugin. Its plays great and excellent framerate except when it loads multiples of the same character. Link vs Link is a little choppy. Team Yoshi(18Yoshis!) is something like 4FPS and even though only three are on screen at the same time emulation speeds up proportional to how many I have killed.
It has no problem with 4 different characters on the screen at the same time so I suspect it has enough memory.
Any thoughts as to why this could be? The game runs flawlessly otherwise and my efforts messing with config file settings have been fruitless thus far.