Yes, the Jedi Order had some issues in the prequels. Their adherence to structure and rules have landed them in a lot of trouble. They were spiraling before the Clone Wars began and after the conflict began, their path descended.
We have just spent some brief time with Qui-Gon, but have seen enough to know that he is different from other Jedi. He has a willingness to be unorthodox, and this is a positive quality. Here are five major reasons why he is the best Jedi:
1. He’s not held back by rules.
Rules can be impediments to get the work done. But there can provide flexibility if necessary. Qui-Gon knew that and was guided by the Force first.
The Jedi Council told Qui-Gon that Anakin was too old and that he was not fit. He saw the boy’s skills and realized that there was a possibility of him being the Chosen One. This gave him insight into the workings of the Force.
Obi-Wan said, “If you would just follow the Code, you would be on the Council,” and from here, we know that business with Anakin was not the first time he challenged the Council.