Doctor Whooves and Assistant/WMG

Knights of Time and Space will be used in an upcoming episode.
Because it's to Epic-Awesome for those two to not use. Listen! Episode Six is supposed to deal with Derpy and the Doctor argueing and their friendship being strained to the breaking point. Having this song at the very end would be the perfect way to end the episode and show their restored and stronger than ever friendship at the same time in an And the Adventure Continues sort of way.

Ditzy's selective immunity to the Psychic Paper will become a plot point.
Episode 5 revealed that the Psychic paper only works on one eye at a time. It would be perfectly befitting both source materials by setting up a future plot point as a seemingly one-off gag. Clearly The Master will show up with the same item and the only pony who either believes The Doctor or sees through the ruse will be Ditzy, because she's partially immune to it.

Ditzy's voice will change at some point.
It's got to, what with The Last Roundup and all.

The Blue Unicorn that the Dr. talked to is his future incarnation
He knows quite a lot about electrical surges... especially since they don't exist in Equestria.
 * He'll be pretty happy about it, since he seems to have some obsession with unicorns.