Whatever role Yoda has in the hierarchy, if any, he can personally train Obi Wan. Obi Wan could have been such a promising student that Yoda took it upon himself to train him.

As for showing the Council, you can make it a centerpiece like in the PT, or something you see once in awhile and maybe see the Jedi council leader more often, who can embody the disgrace of the Council.

If the Jedi are less organized, what is the relation of the Council to the Jedi? Who decided there should be a council and how does it exert influence?