RTD was much better at weaving in subtle hints at an overall arc. The mentions of "Bad Wolf" might have made the Doc or Rose raise an eyebrow, but it was always part of the episode's storyline and not tacked on afterwards. Likewise the occasional references to "Mr Saxon" just came up as part of the dialogue ("orders from Mr Saxon..", etc).
Moffat seems far too eager to pat himself on the back with these grand plans and "oooooh, look, I'm foreshadowing! It's mysterious!!" Most of the time his plots take you right out of the adventure you're watching. Madam Kovarian ended up just being an annoyance. "Oh look, here's a thing to interrupt what you're watching.. yes it's this seasons Mysterious Plot Arc!™"
Exactly. It's too on-the-nose about the plot arc. And it's always just a little tease here and there, which results in him having to reveal the whole shebang at once, which usually means it's a hurried mess of a reveal.
That said, I think of all the Moffat-era seasons...I actually liked this one the best in terms of its overall arc. The arc wasn't really the Missy stuff. The arc was about Clara's growth as a character, her relationship with Danny, and how the Doctor played into that -- as well as really exploring who this new Doctor is. And in that regard, I think they did a terrific job. They might've been able to balance individual episodes a bit more or less on the plot vs. character side, but the character side was masterfully done this year, and the finale really felt...well...final about it. It felt like an excellent culmination of the Doctor's considerations of whether he's a good man or a bad man (he's neither -- he's an idiot who does his best to help where he can, high-fallutin' name notwithstanding). It also felt like a really solid exploration of who this "Impossible Girl" is, and how traveling with the Doctor has affected her. She really came to be a "surrogate" Doctor in a way that began to chip at her humanity, and ultimately, in a way, cost her a real shot at love.
In a way, if the tales of Jo, Sara Jane, and Rose (as shown in School Reunion and, I gather, in the Sara Jane Adventures where Jo appeared) offer an example of why traveling with the Doctor is this amazing, wonderful adventure that should be grabbed with both hands, Clara's story really truly highlighted the genuine threat to one's humanity that a chance to travel with the Doctor offers, and what you give up or may miss out on by going with the Doctor. No other season, for example, has shown quite the degree to which leaving friends, family, and loved ones behind can have such a lasting, negative impact on your life. Rose came closest to it, I'd say, but as with Amy (and Rory the afterthought), you always got the sense that while
other people might've been bothered by it,
she never really minded much, and always viewed it as "worth it." Given how they parted company, I think Clara might have a tough time saying it was all worth it with real conviction, or at least without nagging doubts lurking in the back of her mind. Was it
really worth it? What if she'd stayed home and met Danny and just had a nice, happy life with him? And now...she'll never know, because she was splitting herself between Danny and the Doctor.
I loved that aspect to the story, actually. As frustrating as Clara could be (to me), I still appreciated that they showed the cost to her. And I thought the final shot of her just...walking away...really brought that all home. This wasn't a happy ending, or a maudlin departure. It was a recognition that life couldn't go on as it had before, and that Clara now bore the weight of her choices as she walked off to figure out how to put her life together. Maybe she'll turn out ok. I suspect she would, anyway, but it won't be without some real damage and some real "What if...?" questions haunting her.