My suggestion would be to keep Season 1 as is.
Then take Seasons 2 and 3, and re-cut them into about 10-15 episodes to make a legitimately *good* Season 2 to replace the ones that exist. Then, when Season 4 comes and Bryan Fuller returns, hopefully the show will return to being good, and I can just replace Seasons 2 and 3 on my DVD shelf with this edit.
Bear in mind, however, I stopped watching at around 3.5 or 3.6, so I don't know what's doing with S3, and if my idea can be done. And it started off so promising ...
Based on what I've seen, the main thing that needs to be changed is character motivations. The biggest problem with S2 and what I saw of 3 is that instead of putting established characters in a situation and following how they would act, they changed the characters to make them fit in their new stories. Kind of like sanding down a square peg to fit in a round hole, but I wanted to see how the square peg figured out how to get through on its own without being forcibly changed. If the characters had changed in natural ways, then I'd have been fine with the changing characterizations, but they didn't, so I wasn't. Hiro, Peter and Claire are the two biggest examples of this.
IMO the best thing Fuller can do with Season 4 is have Hiro time-travel to the end of Season 1, make sure Peter dies for real with the explosion thing, killing him along with it, thus getting rid of both time-travellers once and for all, and ignoring the fact that seasons 2 and 3 ever happened. Start anew. The time-travelling was starting to make the show far too convoluted.