I didn't like what they did with Scully in the last few seasons. She went from the skeptic to the believer? Come on. She saw some damn weird things in the first season alone, but it took Duchovny walking off the set to convert her?
I always identified with Mulder (probably why I will end up in a state run institution).
I know I should have observed more from writer's POV, but this always got in the way...