introduced the alternate universe at the very end of season 1. I personally love the alternate universe because it's so interesting and because it gave us the chance for more Leonard Nimoy.
I get where you're coming from, though. It can be hard to wrap your mind around at times. I enjoyed the creature-of-the-week layout during the first two seasons, too, though it is still around during the other seasons. It just takes a backseat.
With that said, Fringe is easily one of the best shows on television and I'm really happy that the Fox president enjoys it enough to keep protecting it from cancellation.