What are your specs? If you post them we may be able to provide feedback. Mainly the cause of stuttering is because isn't running at 100% consistently throughout some areas (may be areas tthat are more demanding than others due to game effects) your CPU could aslo be throtling because of heat issues, or your GPU may be setting a bottleneck for some areas. As far as the controller it is far beter to buy a bluetooth dongle and play with your wii remote and nunchuk, it will save you a lot of trouble with wii games (esoecially motion controls), as far as visual quality goes you can change the screen resolution and internal resolution, as well as anti-aliasing and anisotropic filtering, as well as setting EFB copy to scale for a more crisp image
The right man in the wrong place can make all the difference in the world.