The problem with Fringe is that the only consistently good thing about the standalone episodes is Walter. For my part, the only good thing about the mythology episodes has been the Walter arc. I think most people agree even if they don't realize it. The only thing the mythology episode Peter added was the story of how Nina lost her arm, but it was widely and correctly regarded as the best of the series to date.
If they must have an arc, centering it on Walter (both versions,) is necessary. Which means
1.) orienting Peter to his family issues instead of the pathetic Olivia infatuation
2.) giving Peter a brain (if it still possible to make it plausible) so that the Walter arc has another player
3.) giving Astrid a personality
4.) bringing Peter's mother/Walter's "wife" on stage
5.) trying to retcon away that awful stupidity about First People and the million year plot.