So, the thing about shows, seasons that come off as the black sheep of the flock and Showrunners.
All shows have seasons that are more controversial. That does not make them more or less than the rest, it just makes them different than what's been established as usual for that given show and that given audience. A certain idea will not sit as well with all people, and Season 4 is one of these, especially because it came at a time of such tension as to what the future of the show was. We didn't know if there even was a future to look forward to, and the anxiety derived from that cannot be overlooked.
Life is risk, business is risk, and television is an industry. Fringe stands out because unlike others, it cherishes innovation, thrives in it instead of resisting it in favor of traditional models of unchanging storytelling that would have driven it to stagnation a long time ago. Fringe reinvents itself. If watched separately, every season is an entirely different kind of storytelling, going from one side to the other of the serialized spectrum. Sometimes, the risks you take don't pan out, and you deal with the consequences.
The above does not mean that what will come to be considered "low points" cannot serve as fundamental character development without which further, better seasons can be developed, as seen in our Final Season. Ask Joss Whedon.
Showrunners only have so much control over shows with such sprawling mythology as Fringe. There are only a few possible, logical outcomes. Sometimes, the outcome chosen will look great in theory, but not so much in practice. It needs to be said that television is a process. What we see in our TV screens is an extremely filtered and processed product of hours and hours of work by various individuals with diverse points of view. What's written in the script is its base, yes, but in the end, it's just a small portion of the process (albeit a fundamental one).
Hindsight's 20/20. Shows are written by people and people make mistakes. Sometimes they're only mistakes because the audience couldn't, or wouldn't, receive the message the way it was meant to be. There's nothing to do but look back on it and have the will to do better the next time. Both Fringe and Joel have done that well.
A showrunner has no express need to do everything the show's fandom demands. It's the power of being the producer instead of the consumer. The Product is theirs, what they do with it is their choice wether the audience likes it or not (of course, the audience can then choose to not watch, and the show tanks, but that's a whole other discussion. The relationship will always be reciprocal). Fringe's showrunners have been exceptional in their will to give the audience above par entertainment, and in their attentiveness to the audience's wants. That is something to be thankful for, I think.
Ā AND JUST ENJOY THE LAST FEW EPISODES, BECAUSE WETHER WE LIKE IT OR NOT, THERE IS AN END, AND IT IS NEAR, AND NOT EVERYONE IS GOING TO LIKE IT, AND THERE IS NOTHING, I REPEAT, NOTHING, THAT WE CAN DO ABOUT THAT.