TL,DR version:
 
A typical episode takes about nine weeks to go from premise to polish.
 
Songs are generally planned in the premise or story meeting stage.
 
The Season 3 finale was originally written in November 2011. Twilicorn was a while in coming, folks, and the writers knew they wanted to make it a musical fairly early on.
 
From the finale, no one’s sure what Star Swirl’s spell was trying to accomplish.
 
The Season 4 opener will focus on Twilight’s fears and questions after becoming a Princess. As an editorial note, I have every faith in Meghan and the crew that they’ll lay our own questions to rest.
 
Why didn’t we have a Rarity episode this season? She turned out being pretty mean to Spike in the initial treatment, so the episode went to Applejack instead. And so we got “Spike at Your Service.”
 
When asked about difficult episodes to write for, AKR cited MMMMystery on the Friendship Express because she hadn’t written a mystery before, and the early episodes of Season 1 were a struggle for her to discover each characters’ voices.
 
M.A. Larson has trouble writing Fluttershy every now and then, Meghan can’t get Applejack into trouble, Rarity’s colloquialisms challenge Cindy, and Amy found herself discovering characters she hadn’t written much before in Season 4.
 
Hasbro isn’t soulless. Meghan feels the stories she and the writers want to tell are the ones that get told despite what others believe, and the studio Hasbro built up has animators and other folks who care about making a good TV show in its executive positions. At the end of the day, Friendship is Magic there to advertise toys of brightly colored ponies, but the writers are pretty happy with how much control they have over their episodes.
 
Amy had an episode she wanted to write where Pinkie would spend the day walking around “lollygabbing”, but the premise didn’t go through. Other premises fail when they tread similar ground to older episodes.
 
It looks unlikely that IDW and Hasbro are going to maintain one coherent continuity between the comic and the show. The comic goes to lengths to honor events in the show at least from Season 2 and before, though.
 
Are we getting a Star Swirl episode? The abject looks of confused dismay on everyones’ faces don’t point to anything in the works at press time.
 
Why didn’t Trixie trust wheels in “Magic Duel?” She’s continuing her slow slide into egocentric insanity by that point in the episode.
 
Why send Pee Wee back in “Just for Sidekicks?” This was a storyboarding decision, actually, put in especially to appease those who were gonna ask where that little bird was.
 
Meghan got to ride a horse in a circle when she was around eight or so, while her father and older sibling got to ride into the sunset. She hates horses now.
 
MS Paint is a poor program for writing stories, as Mic suggested.
 
We might see Trixie again. Thanks, Seth!
 
And the last question of the panel came from our very own Phoe, woman of words! When she asked Meghan about developing antagonists that live up to those who came before and raising the stakes, Meghan was very gracious and acknowledged King Sombra’s lukewarm reception in the fandom. She admitted he was her least favorite character she’d written, saying he didn’t come across in the episode as formed as she had him in her head. He was always meant to be more of an evil presence (think Sauron) who doesn’t share the same in-your-face presence as Discord and Chrysalis, a sentiment Phoe identified accurately in her thematic analysis of the premiere back in November.