NuWho's Missed Opportunities

The Moffat era of Doctor Who just ended, and as he was a key writer during the Russell T Davies era, one might say it's the end of sequence that started way back in 2005. So let's open the Book of Truth and look back at the past 12 years to identify what I consider NuWho's missed opportunities. (In chronological order.)

The identity of the Toclafanes. In The Sound of Drums, the Master tells the Doctor that the truth will make him cry, and the Doctor recognizes the name of the Master's nasty allies from the ends of time as a Gallifreyan fairy tale. Turns out, they were the last of humanity (as seen in Utopia, just the week before). That's not all that shocking or tear-worthy given half the villains in Doctor Who are plain old humans. We're jerks. RTD missed a massive opportunity to bring back the Time Lords right then and there (the title The Last of the Time Lords was, in fact, perfect for it). Time Lords that would have escaped the Time War by converting themselves into little balls of metal. The Time Lords the Doctor had been sad about for three series, and when they're back, they're evil monsters. It's epic! It's ironic! In the end, he would have had to destroy them a second time... It's tragic!
What we would have lost: Nothing. If these were escaped Time Lords, Gallifrey could still have appeared in The End of Time, The Day of the Doctor, etc.

Jenny. When the Doctor's daughter came back to life and left her little planet, there seemed to be every expectation that we'd see her again some day. Though Big Finish audio is doing something with the character now, it seems a shame that she didn't cross paths with her dad (now no longer played by her husband) during Moffat's run. Kind of a River Song type without the romantic baggage, you know? Having her MEET River (two daughters of the TARDIS) would have been cool. Also, to have spelled it Gennie, for Genetic.

The Tenth Doctor properly regenerates at the end of The Stolen Earth. For an episode that ends on such a brilliant cliffhanger, it's followed by massive cop-out that led to a pretty terrible alternative - the Doctor sends his regeneration energy into his loose hand and makes what we call "Doctor Blue", who is then dropped off in the parallel universe with Rose who doesn't seem that happy about it. It's stupid, it creates a terrible precedent for regeneration ex machina, and it left everyone with an icky feeling. What should have happened: The Doctor regenerates right there just he catches up to Rose. Becomes another man, one who doesn't share the same feelings. Really, the only way to end the Ten-Rose relationship conclusively after the way it got built up. It's got all the heart-wrenching attributes of a RTD script, and would have been a huge surprise at the time, since no other actor had been announced.
What we would have lost: While I really don't care about the Year of Specials that followed, we really don't want to lose that final scene with Donna in Journey's End, which wouldn't have worked as a new Doctor's first episode. And then there's the casting of the 11th Doctor which would of course have been different.

The Yeti. In 2010, Doctor Who designer Peter McKinstry showed his technical drawing for a Yeti redesign giving us hope that one of Classic Who's recurring monsters would make an appearance in Series 5 or 6. While we've seen the Great Intelligence, it was NOT accompanied by its fluffy minions. Deep sadness.

The Ponds leave in The God Complex. That was a perfect ending for Amy and Rory. They've just been through an intense psychological experience, learned things about themselves and their need to nest, and an insightful Doctor drops them off at their very own house, with a blue door, no less. Lovely. Didn't mind so much when they cameoed in the next episode. The finale too, it worked. Christmas special, they're not there. And then they return for half a series, undoing that moment. It's not as egregious a misstep as some of these others (because they still used their home life in the stories), but I've found that any more than two series and the companion has perhaps overstayed their welcome, any less than two makes you wish you had more.
What we would have lost: The Power of Three is maybe the only one I might miss outright, but it's a stay at home episode that would have worked as a Doctor-lite in that next series.

Ian Chesterton as Coal Hill School's headmaster. When Coal Hill made a comeback as Clara's place of employment, who else thought for sure we'd see Ian either as headmaster, or visiting retired teacher? In fact, why HAVEN'T they used William Russell in any episode of New Who? You'd think there would be an imperative to use the oldest surviving companion before it's too late to do so. Did that line from Sarah Jane Adventures about the Ian and Barbara's apparent vitality screw that up? Cuz it sure doesn't sound like more than a rumor.

Clara leaves in Last Christmas. Another companion who had a fine ending, and then came back anyway. Last Christmas has a sequence where Clara wakes up from Doctor Who's version of Inception to find she's an old woman, dreaming of her youth. That would have made for an unusual companion departure (her actual goodbye in the previous episode anyway), someone who went on to live her life, and that we didn't have to wait 50 years to see again. Jenna-Louise Coleman was even set to go, wasn't she? Anyway, big cop-out, wakes up from THAT dream and she's her youthful self. Oh well.
What we would have lost: It's hard to imagine The Zygon Inversion or Heaven Sent without the strong Twelve-Clara connection, but the way Bill was so readily accepted into the Doctor's heart and ours, I'm sure they could have made do.

Companion goodbyes in Twice Upon a Time. I just mentioned this, but it bears repeating. How hard would it have been, when Clara makes her final appearance as a Testimonial ghost, to have silhouettes of every companion since the beginning behind her, backlit by the sunrise? A lot of people in fact expected Susan to show up in place of, or in addition to, Bill, ever since we saw her picture on the Doctor's desk, in fact. It would have changed the story completely, and with the fresh start, having her regenerate and become an upcoming companion was probably not in the plans. ("Why does she keep calling you grandfather?") But since presumably all companions ever are dead by the year 5 Billion and Change, they could all be stored in the Testimony, and could have said their goodbyes here. I'm disappointed they didn't think of it.

Those are my picks, what are yours?