If you asked me to pick my absolute least favorite episode of Doctor Who across its entire history then I would definitely pick "Power of Three." It's not that it's a bad episode exactly. It has more to do with how much of a cop-out it is. Amy and Rory come to terms with their desire to keep traveling with The Doctor, even giving us a cheesy but moving ending monologue on how powerful they are as a trio. The very next week the whole thing was rendered moot by "Angels Take Manhattan".
Now, that was deeply disappointing in terms of what we saw on the screen, but it was also an example of something brilliant the revived show has consciously introduced to Doctor Who that is almost entirely absent in the classic show. Basically what we saw was the creation of a narrative gap where future stories can be set.
In the years between the series cancellation in 1989 and its revival in 2005 Doctor Who existed in the form of books, comics, and audio stories. Though these are now just excellent supplements for the continuing show for 16 years they were all fans had.
At first it was just the continuation of the adventures of the Seventh and later Eighth Doctors. It wasn't until 1994 that Virgin realized that there was money to be made and stories to tell in its Missing Adventures line focusing on Doctors before the "current" one. BBC followed suit after it took the license back and founded the Past Adventures line to coincide with the Eighth Doctor Adventures. Big Finish expanded the idea when it began producing audio plays featuring actors from all across the show's history in its dramas.
These present a problem, though. Gaps where you can insert truly original stories featuring, say, new companions for old Doctors are very rare in the classic series. For instance, Big Finish introduced Oliver Harper as a new companion to the First Doctor, but he is an addition to the Tardis crew consisting of the First and Steven Taylor set after "The Daleks' Master Plan" and before "The Massacre of St Bartholomew's Eve".
For the most part the first seven Doctors went directly from companion to companion with no gap. You can't, for instance, really send the Second Doctor and Jamie off on their own after Ben and Polly because they lose the Tardis in Ben and Polly's last adventure and don't get it back until they pick up Victoria in "Evil of the Daleks". The only way to really craft an original story for Troughton's Doctor where you can explore wholly new territory is to shoehorn it in the nebulous time between his sentence of exile by the Time Lords and the moment when the Third Doctor falls out of the Tardis, something that's always come across as extremely awkward.
There are a few good ones. The Fourth Doctor traveled alone in "The Deadly Assassin" and can have any number of travels between the end of that serial and when he meets Leela in the next. Thanks to the quirk of Mel being from the Doctor's future and an assumption that he returns her to her proper time to go meet her at the appropriate time after the Trial of a Time Lord story arc there's a huge open space to create wonderful new Sixth Doctor tales. Big Finish did exactly that, giving him Evelyn Smythe as a new companion and later teaming him briefly with the Eighth Doctor's companion Charley Pollard. These are notable exceptions.
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Almost since the show returned in 2005 the writers have been very careful to leave their Doctors room to grow outside of what we see on screen without sacrificing space for additional stories with established companions. The Tenth Doctor and Rose could still travel together in any number of future books, comics or -- fingers crossed -- audio dramas. On the other hand Ten can and has used the periods when he was clearly on his own to meet new companions in comics like Heather McCrimmon, Majenta Pryce and most recently Gabby Gonzalez.
That's why "Power of Three" happens the way it does. The Eleventh Doctor is free to go wherever he wants before the events of the episode free from Amy and Rory, but also has a gap where he can have them along until they are lost in "Angels Take Manhattan". As annoying as it sometimes is to have Clara not actually traveling with The Doctor full-time it does leave blank pages for future writers.
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The same goes for the War Doctor. It's not a coincidence that the Eighth Doctor regenerates into a young man in "Night of the Doctor" and that we see the War Doctor otherwise only at the end of his life. His era remains open to exploration in books or in his specific case with a wholly different actor without upsetting established canon. You just need a guy that looks like an indistinct mirror reflection of a young John Hurt and you're good to go.
And that's important because television is still television. As much as I hope that Doctor Who exists uninterrupted for the next 50 years and never again goes through a dark period where it doesn't it probably won't happen. The odds are one day a Doctor will walk off screen and it will be a very long time before another walks back on. The people writing for the show now know this. Many of them cut their teeth writing for The Doctor when it was off the air.
So they're obviously very careful to make sure there are cleared spaces to build upon. The long term future of Doctor Who will probably depend on it.