I think that the main flaw of the merit-system is that it lured all the attention of bitcointalk participants, leaving in the shadow the main topics devoted to the most important and initial issues of the forum. This system was intended as a motivation for improving the quality of posts, whereas in fact it resulted just in an increase in the number of comments. All conversations revolve around merits. Part of the participants are in pursuit of merits, and the other part writes about what exactly the first ones do wrong and why they don`t receive merits.
Instead of encouraging forum members to write more vivid, constructive and interesting posts about crypto-currencies, economy or trade, the merit-system drove the participants into a vicious circle. After all, in general, people receive merits for posts, one way or another devoted to merits. The merit-system features were misunderstood by the majority of bitcointalk members, and that`s how I see the main flaw.