Gosh, that sounds like a real big mess of a project. Even the creators of the show have been struggling with that.

I haven't seen season 5 yet, but in season 4, they were trying awful hard to get back to stories from the comics that the previous seasons had skipped, and to flesh out characters who had been in the comics since the beginning, but in the show, had only just been introduced. Seems like it would be a nightmare to try to rebalance the first three seasons, and it would be impossible to slow down the new characters' storylines to a sensible pace.

Also, I would think you'd have to pull a LotR and change where each season begins and ends, since IMO season 2 has the most "filler".