One example that comes to mind is The Blunder Years. I like the episode, I think it adds depth to the character of Waylon Smithers and the story is interesting but it suffers a lot from coming out late in the series.
Many of the jokes don't land and they waste too much time with Homer screaming and Marge being obssessed with the paper towels guy.
If the episode had been produced during the Oakley/Weinstein era I think it would have been a lot better.
What other examples can you think of?