The big flaw was that D&D 3e was not Powergamer-safe. It would work wonderfully if the PC's weren't trying to abuse/break the system and were having a fun, relaxed time. The potential abuses in the rules (usually involving multiclass combos or being very literal with the wording of spells or feats) were huge, and I saw some people make the rules beg for mercy they bent and twisted them so hard.