I like M1 because the shock and defeying reality.
M2 was good for going in depth as to what the Matrix is and the suspense of the looming battle and Neo's fate.
M3 was good for the massive battles and wrap-up.
Each of the Matrix movies are good in their own way. Each one was designed to be special in it's own way, so comparing and seeing what one is best is difficult. One might have a good story line, while the other has good special effects. It depends on how you want to judge them. each person has their own way of viewing and their favorite element.