I think at that level of bike, the shifter has more to do with the smoothness than the rear derailleur (all things tune-upwise being equal). Other things that effect shifting include routing of cables, type of chain, position of chain before shifting, chainline alignment, spacing of gears in the cassette, quality of cassette. Some of these things can be adjusted and tuned and others can be made better by swapping components but things like cable routing might not be changable. There are some supplemental devices which help improve shifting too such as the Avid Rollamajig.
Did you do an absolute one-for-one comparison by keeping the shifting circumstances (load, gear-to-gear position, etc) consistant?