In as few words as possible: focus.
Now to elaborate, for any fringe fan, you'll recognize that most fringe episodes consist of a standalone plot, in which they have to solve some weird mystery and then it's usually related to the overall plot of the other universe and its issues related to this one. That's all good and nice, but it's not sustainable - we're midway through Season 3, and there's not been a whole lot going on. It feels a bit like Lost in that Lost started out really slowly and by the end of it, it had lost control and random shit was coming out of nowhere.
Don't mistake the fact that I loved Lost, but Abrams needs to do Fringe better. What Fringe needs to do is choose an endpoint and stick to it. They need to choose whether there's going to be a flat out war between universes, or if it's going to be a more subtle, character-based resolution to the problems. But most importantly of all, they need to explain their shit.
My biggest complaint with Lost was the amount of mysteries that went flat out unresolved. Fringe has been doing a much better job of keeping the unresolved mysteries to a minimum, but it's not at zero. What happened to the empath who was chilling with the observer in the first season? What are the shapeshifters, and why is there no mention of them on the other side? And what about that room where the teacher was training the cortexifan kids? What the hell was up with that? The fact that Fringe is currently in question of being renewed for another season makes me worry - there's no way they can adequately handle all the plot points and answer all questions and sum it up this season. It's just not possible.
But I want them to start. Then, I'm also torn on another issue - recap episodes. I hate them, but I think a recap/explanation episode would be great for getting new fans, but it should be advertised, or maybe even just have "An Introduction to Fringe" as a TV special and advertise the hell out of it, so the show can get some new fans.
Overall, the show just needs to get its shit together. I love it, and if it ends, I'm going to have to punch someone.