Season 4 was a great season of TV entertainment. Among the top TV shows on television currently. But I feel it wasn't as good as Season 3.
I'm not sure if I can pinpoint on it why. I feel the characters in season 3 ("evil" Walter, fake Olivia) were a bit more gritty and real. They had more depth. The story seems to flow better. Like the series Lost, in Season 3 the characters motivation were more clear and thus dramatic. You could feel their dilemma. I also like the character conflict better in Season 3 especially between the red and blue universe characters. Even Newton vs fake Olivia was pretty good 1 to 1 character interaction. Olivia vs fake Olivia. Same as Walternate vs the red Fringe teams, Brandon, the interaction between the red Fringe team, etc. The plot of wondering what Walternate/fake Olivia/etc were up to was better too.
The mission and motivation of all the characters seem to be better in Season 3 than Season 4.