I've always thought that the synthetic route taken to obtain the MDMA makes a difference in the qualitative effect. First of all, different syntheses will give different ratios of S and R enantiomers (as Dr. Tox brings up), and it is known that the S and R forms are both active but with slightly different effects. The S enantiomer of course is said to be the more active form of MDMA, and you might expect it to be a little more stimulating since it is also the S enantiomer of methamphetamine that is the more active form. The R enantiomer is the more active form of psychedelic phenethylamines, including MDA, and in MDMA the R enantiomer is reportedly a little mellower in effect (but maybe more psychedelic?).
Also different synthetic routes can leave some quantity of side reaction products if the chemist doesn't fully clean it up, which can have an influence on the overall effect depending on which ones are present and at what concentrations.
Also different synthetic routes can leave some quantity of side reaction products if the chemist doesn't fully clean it up, which can have an influence on the overall effect depending on which ones are present and at what concentrations.