Were Targaryens midgets?
Considering how short Jon Snow and Daenerys' actors are, and those theories about Tyrion being a Targaryen, what if they cast Kit Harrington and Emilia Clarke on purpose because they were short to hint at Jons true identity?
In an earlier season Tywin explains to Joffrey that over time the dragons shrunk in size until the last dragon was no bigger than an apple. Maybe too, the Targaryens shrunk over time.
Also as a stroke of luck, to emphasize Jon Snows different parentage, all the Stark actors grew up to be tall, minus Arya but this fits in with the book where Arya felt different because she wasn't pretty like Sansa and secretly feared she was a bastard too which is why she was closer to Jon.