One of the reasons, I believe, the .36 had the better reputation is when loaded with a round ball, it had a higher velocity. A few years ago Ed Sanow ran ballistic tests on the percussion revolvers and the .36 was no slouch with a RB....seems it was in the 50-60% in one shot stopping using his formula.
Elmer Kieth spoke highly of the old Navy .36 and stated it was a better stopper than the 38 Spl. (158RNL). The round ball may be a bit less efficient in punching through the human body and may have been more easily deflected too, which would cause a bad internal wound....don't know, but I don't want to be on the recieving end! I'll trust the old timers word.
Also, shot placement is a better key to 'stopping power', IMO.