Oh, it was. Frequently. The arc was about misdirection so it was easy to not take note of it, but it is very much the core of series 7. For example:
it’s genuinely obvious and brought up again and again and again.
The Bells of Saint John – the monks term it “his madness” in what is a disturbing set-up (hiding away just to think about her and paint her?)… and the entire arc is giving a nod when one of Clara’s first words to him is “Just Clara Oswald”
The Rings of Akhaten – Clara explains that she will only travel with the Doctor as herself and not the ghost of someone else
Hide – The Doctor’s quest for the truth ends in Emma telling him that “she’s a perfectly ordinary girl” and asking him whether that isn’t enough, while warning Clara away from the Doctor
Journey to the Centre of the TARDIS – The Doctor’s obsession with her identity is portrayed as scary, see above
Nightmare in Silver – The Doctor’s obsession with “The Impossible Girl” is potrayed as downright creepy
And it all culminates in The Name of the Doctor, where the Doctor doesn’t solve her mystery at all. Instead, Clara needs the knowledge about the echoes (”secrets keep us safe”… not) to figure out for herself what is happening and making a choice to save the Doctor.
I could link to at least a dozen posts which make the same point, it’s been the dominant lense of analysis of series 7 part 2 for years now. Because taking into account what is happening and making any normative judgement about the Doctor’s behaviour, the fact that he’s wrong isn’t a mystery.
