First of all it soesn't completely eliminate the stuttering, but it reduces it to the minimun possible (I have almost no stuttering when using those settings, this makes the game a lot more playable for people who can't stand the stuttering like me, so basically the emulation is almost perfect), But it requires a Very strong PC to get full speed.
My settings are: I enabled Fast Depth calculation (doesn't cause problems in the game), disabled dual core and idle skipping (that's why it requires a very strong pc), disabled bounding box too. I also unticked Ignore format changes, and skip efb access from cpu (don't know if they change anything).
the stuttering in the motroid prime series always freaks me out, and with those settings the games is almost stutter free (after the first times you do some basic actions like shooting, using the morph ball etc) and the emulation (graphics and sound wise) is perfect! (please note that in the first minutes you will encounter some stuttering because the shaders haven't been cached yet, but it's really pretty minor)
Hope it will help
it's really a night and day difference for me.
Edit: I have Windows 7 X64, and I used OpenGL. I have GTX 980 (I don't know how AMD cards works with OPENGL)
My settings are: I enabled Fast Depth calculation (doesn't cause problems in the game), disabled dual core and idle skipping (that's why it requires a very strong pc), disabled bounding box too. I also unticked Ignore format changes, and skip efb access from cpu (don't know if they change anything).
the stuttering in the motroid prime series always freaks me out, and with those settings the games is almost stutter free (after the first times you do some basic actions like shooting, using the morph ball etc) and the emulation (graphics and sound wise) is perfect! (please note that in the first minutes you will encounter some stuttering because the shaders haven't been cached yet, but it's really pretty minor)
Hope it will help

Edit: I have Windows 7 X64, and I used OpenGL. I have GTX 980 (I don't know how AMD cards works with OPENGL)