understand ...
Being a 'Born-Again Scaper' myself [one who came into the show later than the beginning and was hooked], I think some of the problem was the show got too 'internal' toward the end of S3 and the beginning of S4. If you didn't watch every week, you couldn't follow what was going on.
Interestingly enough, those same concerns were voiced by a couple of the actors I had a chance to meet last Jan in Australia - that the scripts had become very 'in' and if you didn't follow things very closely, it was easy to get turned around.
rowan