I completely agree with you, writers think they are being clever and make things too complex for themselves and then have no way to get out of it. Personally, this is why I am starting to prefer the format of cable series like the ones you mentioned. They typically have a smaller season, anywhere from 6 to 12 episodes, and so they are able to get away with having every episode be entirely story arc based. There doesn't need to be any "filler" episodes. That is when you run off the track with traditional 20 something episode shows, there is too much filler and you lose track of the overall story arc. When weekly plots and overall story arc are combined well then the show works, when it becomes more filler than anything else is when people start to lose interest. And I fear that is the direction Fringe is taking, and unfortunately for them they are on Fox...which has a tendency to pull the plug on a show the second its ratings start to diminish, and they are already on Fridays which is considered a day of death for network shows. So it appears that as far as the network is concerned, it is already fizzling.
Another problem that I feel Fringe is up against is needing to hit an 11. Last season they were on the top of their game and in my opinion the show was at a perfect 10, it was excellent. But now they are trying to reach for the 11 instead of just maintaining a 10, and that is a good way to fail.