I guess I can see that. Looking at my own list, some of my own episodes are either kind of dumb (Discord starting a Disco dance hall) or else way too dark (Pumpkin Cake being a victim of SIDS).
So I guess I'll just post my "Best Three, " the ones I would actually like to see (or perhaps write as a fanfic):
Episode 2 - Romantic Blues Pinkie Pie visits a fortune teller who gives her a vision of her future husband. Rather than being happy, Pinkie realizes she's still too immature for such a thing and starts avoiding men to prevent the prophecy from coming true... and then the man from the vision appears.
Episode 10 - Applejack the Unicorn Just what it sounds like: one day, Applejack grows a horn. How will she adapt to her newfound magical powers?
(Elsewhere in the list I had a story about Derpy body-switching with one of the mane cast... perhaps the two premises could be combined?)
Episode 12 - A Child in Bloom This episode takes place years in the future. As a foal, Apple Bloom was put in an arranged marriage with a colt from another farm. Now she's of age and the colt has come to complete the bargain. But Apple Bloom is in love with somebody else. The twist is
she averts the Hollywood Ending and goes with the arranged marriage, which turns out to be the right move because she later learns that her "true love" was a drunken alcoholic with schizophrenia
.... You're all probably glad I don't write for the show, aren't you?