2. Series 6
Stephen Moffat came into his time as showrunner on Doctor Who with a plan, and Series 6 seems to be the place where all the pieces came together. There were no bad episodes in this season, and the question of River Song's relationship with the Doctor plays out beautifully.
The inverse timeline might have been too complicated to follow in a less cohesive season, but the slow trickle of information, along with major reveals in episodes like "A Good Man Goes To War," make it believable for the Doctor to begin the season telling River to her face that he doesn't trust her and end it by marrying her.
In addition to solving a multi-season mystery, Series 6 shows what happens when the Doctor is tempted to give up his moral code. What feel like typical "badass" moments suddenly become heartbreaking when it becomes clear that the Doctor has become a symbol of fear, not hope.
Between the relationships between characters, time travel hijinks, and fun quips, Series 6 is written for fans who grew up with Doctor Who, challenging them to think about whether the Doctor is a hero or not, and whether they should trust him as much as Amy does when so many tragedies seem to follow in his wake.