All of your graphics issues have been discussed at some point or other on these threads. The stuttering animation can be improved by using a fps limiter. There is a simple version floating around the web called "FPS Limiter 0.2.rar". You can search for that and try it. The site where it was first released has been down for a while.
Limiting your FPS will also help with mouse movement in the menus.
AA has never worked right for a majority of people and there is no guaranteed workaround atm. Some people have had luck by lowering their AF to 4x and having SSAA enabled in a program like nHancer, but this didn't work for me.
The good news is that most of these issues should be fixed with the expansion and the corresponding patch for D2! You just have to wait till that comes out. I am playing The Witcher until the patch comes out since I can't stand the jaggies!
