I spent a few weeks catching up on Doctor Who, and other than the usual good acting and stories mixed with the occasional gigantic plot holes, I’ve noticed something missing.
The Doctor needs new recurring antagonists that are morally ambiguous.
The bad guys on the show are almost always pure evil, with no shades of gray. Not only that, but the most popular villainous races — the Daleks, the Cybermen, the Sontarans, and so forth — have gotten incredibly silly. (I’m sick to death of the Daleks. They fucking suck, people. Get over it.) The Doctor’s malicious archenemy, the Master, has become a joke; he’s supposed to be out of regenerations, but he keeps coming back. Out of the new crop of villains, the Weeping Angels are great, but work best when used very sparingly. But even then, they’re simply malevolent.
So the Doctor clearly needs someone who will clash with him, but whose motives and morality will constantly remain unclear. They might even end up working towards a common goal more often than not, but still be shrouded in mystery and confusion. Shades of gray make for much more interesting storytelling than the simple “defeat the bad guys” trope.
My recommendation? Faction Paradox.
I know Faction creator Lawrence Miles would likely never permit this, but for the sake of argument, let’s pretend it’s possible.
In a nutshell, Faction Paradox was once one a powerful house of Time Lords that went rogue. Now, they muck about in time for their own purposes, using unique time travel methods, alternate universes, and bizarre rites. The Doctor’s faced plenty of nefarious time travelers before, but none quite like these guys. What the Faction is up to is never clear-cut, and if portrayed correctly, they wouldn’t always be the bad guys. They’d equally be good, bad, and anywhere in between. That’s the entire point of their existence.
Faction Paradox first appeared in many Doctor Who novels featuring the Eighth Doctor, but later spun off into their own series. The reason for this is that their “swan song” in the Doctor Who novel The Ancestor Cell was godawful, and Miles has stated that it most certainly does not count in continuity. (Miles did not write Cell; it was handled by Peter Anghelides and Stephen Cole in order to close the Doctor Who Faction storyarc.)
Faction Paradox was explored much further in their own series, and their robust history, politics, and character would be a perfect fit for the current Doctor Who series. Their motives are never black and white, and while that may not be easy for the series’ younger viewers, the adults would certainly appreciate it. I beats one-dimensional baddies like the Daleks and friends any day of the week.
If nothing else, robed villains in skull masks would sell quite a few action figures.

“What? Do I have something on my face?”