No secret whatsoever: the number one reason people hate this story is the flippin' ending.
It's not the number one reason I hate this story, but it's certainly up there. Those of you who have gone on to read "A Short Story by Twilight Sparkle" have doubtless perceived the autobiographical inspiration in Twilight's experience, particularly this part:
...the whole ending felt shockingly rushed and weak, because, frankly, I was so darn tired of writing it by that point I couldn't see straight. I had testily sworn to myself that I would not endure another morning with that stupid "Tea" story hanging over my head...
...which is, of course, all true of me. That said, it's not like another day of writing it would have "fixed" the ending, either. It's been like two years now (insert shocked-dismay emoticon) and I have yet to come up with a "better" ending that feels right.
So. Message received, from like hundreds of you. You hate the ending. I get it. I hate it too. It's too late to edit the original story, but if it had a sequel, what do you most want to see in it? What, specifically, chafes your gizzard about how this story closes? The general lack of all-around happy? That Twilight doesn't get her just desserts for an entire evening of torturing Celestia with the memory spell? That, in a world where you can literally turn birds into oranges, that some kind of solution wasn't forced using unicorn magic? What?
Please note that the characters will remain kind of panicky and stupid, so if the fact that the characters are panicky and stupid is your major beef, I'm afraid I'm not going to be able to accommodate a fix of that nature.