Well, as for the guilt trope, I suppose writers are reacting to Mulder's obsession with the loss of his sister, the rejection by his parents, the havoc the search and associated adventures have on Scully's personal life, etc. There are plenty of reasons for a guilt complex (think of his hallway behavior when Bill Scully calls him a "sorry son of a bitch"), but I would say he handles himself well despite all that. He is energetic, determined, focused, and pretty funny at times.

I've heard English fans criticize the notion of Mulder taking lit classes at Oxford if he was into law enforcement. It does seem like a kidnap from DD's own past. But it never bothered me a bit.