The reason Dinah from "Pony Puppy" is so huge is because she's the size a real-life dog would be next to the pony dolls!
That would mean Megan is about 6 inches tall.
If you believe the ponies live in another dimension, maybe Megan becomes smaller?
Why don't the Twinkle Eyed ponies fillies have eyes like their mothers? They were never forced to be slaves, thus going blind and having to replace their eyes with gems. Alternatively they're copies of the younger versions of the ponies, before they became blind.
Why are there so few stallions in the G1 toyline? Because horse bands are made mostly of females with typically one adult male. The only males we see are foals like Lucky, stallions with families like the Loving Family ponies, and groups of males like the Big Brother ponies. This is supported in other media like how the cartoons stated the boys are running around, and the British comics had the stallions living away from the girls. This could also explain why there are no males in G3; they live away from the females.
Applejack from My Little Pony is notoriously clumsy and always bumping into things. Names in G1 related to their personality, things they like, or their Cutie Mark. There's a liquor made from apples called "Applejack", and Applejack's favorite food is apples... Think about that one for a moment.
For some reason none of the ponies in the first special ever pop up again in the cartoon adaptation. Considering the fact everything is out to kill everypony in G1, it makes you wonder what happened to everyone.. Firefly's rather head-strong and a Leeroy Jenkins, Applejack is a klutz, and Ember is a naive filly.
Ponies never seem to care about whatever tragedies or misfortunes they recently encountered. Considering that almost every episode, special, movie, or comic seems to revolve around them either nearly being killed or enslaved it's possible they've gotten used to the troubles. It makes their world seem rather gloomy.
created an entire website dedicated to fielding questions about it (currently archive only, thanks to Geocities imploding).