My wife will stop watching the show with me when we get to the seasons with Doggett (she's hated Robert Patrick since T2)
She is really missing out !
The great thing about Doggett is that he's his own character. He's not a Mulder substitute. Doggett is a character who hates cover ups and being lied to by his superiors so he uses the X Files in hope that he can bring them down with what they contain. Mulder's reason for being on The X files was simply to find his sister. And, boy, did that story get old....In fact, even in the movie, they refer back to his sister.
And, when it comes to story arcs, I prefer the 'Invasion of the Body Snatchers' type super soldier story to the black oil storyline.
There are some great episodes in series/seasons 8 & 9:
Alone
Scary Monsters
The Sunshine Days
Roadrunners
Medusa
This Is Not Happening
Redrum
Three Words (which is great for Mulder and Doggett conflict)
Essence
Existance
John Doe (Okay, I'm the only person who likes this episode)
Lord of the Flies
Audrey Pauley
Improbable