I know I'm late to the party... but what the heck.
Since you asked, Time Lords (or whatever you call them in this work) are so powerful and ancient and alien that they are not at all like humans in either body or mind, their resemblance is only an illusion.
Or you can explore how much depression and Paranoia Fuel comes from monstrous aliens and enemies always appearing to be wiped out before coming back again (the Daleks, Cybermen, Master, Great Intelligence, etc. and whatever your Expy versions of them are).
Oh, and don't forget the horrifying and mind-melting implications of living in a universe where time is so unstable and constantly changing!
edited 13th Nov '17 2:18:29 PM by CaptainColdCutCliche
Crazy Kiwi
Also, the monsters would be far more terrifying - there's no actual need for your equivalent of Daleks and Cybermen to talk to one another audibly within earshot of outsiders unless - and you can make it clear that they are doing so to deliberately intimidate if you do have them "discuss" the fate of their prisoners aloud.
As critters in hyper-advanced tanks and linked robots respectively, they could communicate in secret and then act in concert without the protagonists being aware of what's happening.
After all, the average foot soldier has no idea what plans are being discussed by tank crews...
OK, we could say that a lot of the time when Daleks communicate and we can hear them they are not really audible, but they seem to communicate in exactly the same way when there are outsiders present who can understand them thanks to the TARDIS's telepathic translator widget. Having them say nothing and then act as a cohesive unit would be terrifying.
Having them say "take the prisoner for interrogation" aloud in the prisoner's presence is Intimidation 101 and all the nastier if you know that they didn't have to say it aloud in order for it to happen...
On a world with no name, (maybe it shall have one, probably not), two commercial time travellers (they deliver product a millisecond before your order is processed), who shall be known as Owen and Bill (because every active time traveller takes a false name or a title, makes it harder for folks to kill you when you were young or do similar tricks) are blacklisted from their world's Society Of Time Travellers for one and a half millennia. Now being blacklisted is a punishment that stretches down to the genes, no time vessel of their kind's make will let them pilot unless accompanied by unblacklisted members who are on board of their own free will.
Note the story takes place in a different fictional universe than Who so no need to take "canon" into consideration.
After a few years fuming the two decide "screw this" and steal two newborns (although they look and act five or six, imagine if Lungbarrow style looms created much younger looking product, also they shall be called the Boy and the Girl, or Clara and Dylan) future members of the Society, using them to gain access to a Time-ship (who's rather annoyed by the whole thing) and head of into space-time.
They are pursed by the Warden and the Statician (who's pissed that they've messed with the census), our other protagonists.
The story spans two thousand subjective years and is an exploration of how wandering adventureres would likely affect a wide universe, whether the Doctor's philosophy of "go against society and be awesome" is really worth pursuing, or maybe he (and by extension Bill and Owen) should have been captured by their respective societies.
Basically anyone who's ever had a niggling thought about the Doctor Who franchise, explain it at will.
Was Once Zolnier Also a cowboy, and a Doctor.