Lets discuss how this awesome episode will impact our fandom.

Just quick:
(1) Changelings living openly in Equestria.
(2) Sweety Drops confirming that the Crowns do have a shady side, down to having black ops.
(3) Stephen Magnet being a part of society.
(4) The Doctor.
(5) Derpy being officially named Muffins.
And many more.

Changeling living openly in Equestria. Singular. We don't know if this implies the presence of more. But if nothing else, it does show that the ponies of Ponyville are no longer as xenophobic as they were back in season one. Town-wide character development has taken place as a result of Zecora, Iron Will, and other friendly non-ponies coming to town. So that's neat.

Out of show, I think this may have been included as a reference to reformed-changeling-in-Equestria fics such as A Novel Tale, Smoke and Mirrors, or my personal favourite, Changeling of the Guard. Given that I also consider the comics to be canon, and Chrysalis and the changelings in the comicverse were certainly not on good terms with Equestria when they were last seen, I take this as an indicator that this changeling is a lone entity, and one who has a backstory similar to the stories portrayed in one of the above-mentioned fics. This changeling's presence does tell us one major thing about their race as a whole, though. They do have individuality and can survive independently. This doesn't necessarily crush the hivemind theory, but it does mean that the changelings are definitely more than just extensions of the Queen's will, and if they do have a hivemind, it's not one that they're enslaved by or irrevocably bound to.

As for the Doctor, it's important to note for those who aren't familiar with Doctor Who that the comparison here doesn't match up 1:1. Despite the comment about being centuries old, the Doctor here is clearly not literally a time lord. In Doctor Who lore, the time lords invented time travel eons before the Doctor himself ever came to be. He was born on their planet, Gallifrey, and ran away after stealing a time machine called a TARDIS, which is bigger on the inside, a living thing, and is described as a pandimensional being in itself. The fact that the Doctor here was apparently born in Equestria, was (is?) trying to invent time travel himself, and does not have a TARDIS, suggests that while he's a really obvious Doctor Who reference, that's all he is. A reference. Not literally an Equestrian version of the legendary time lord hero. Though that's not to say that he hasn't had a few amazing adventures himself, and with age spells being a thing, he may very well actually be centuries old.