I think it probably has something to do with the fact that the afformentioned clubs better players are ageing, and therefore losing some of their stats... such as speed, acceleration, etc... They always tend to make pretty poor signings aswell, resulting in the clubs downfall.
On my save Man U were poor in the first 3 seasons, but the special one took over, and they've been in the top 4 ever since. City are always battling for the title aswell, and always give me a run for my money. Liverpool are atrocious, and Chelsea are starting to come good again after 2 poor seasons. And Arsenal have been on fire for the last 2 seasons, with their younger players coming of age.
As I said, I think it's down to a combination of age and poor/good signings that determine how well these teams perform.