I have a lot of concepts that have been bouncing around in my head recently for MLP episodes. Here's a batch I cooked up in the past week or so, all of which are connected.

"A Study in Pinkie"

Pinkie clone in the adjacent diner booth S6E9

Return of the Clone(s)

Concept/Synopsis: Manehattan mysteries are no match for Private Eye Pinkie Pie, who solves mysteries and conundrums in her own Pinkie way.

Extra Details: The title is a reference to A Study in Scarlet, the first Sherlock Holmes novel, as well as A Study in Pink, the first episode of BBC's Sherlock. Similar to "Rarity Investigates!", the episode will be stylized to pay homage to the Holmesian style of mystery rather than to the film noir style of mystery. Final shots of the episode: After a job well done (and 20 minutes of episode time), the camera pans away from Pinkie to the Manehattan station as several ponies emerge, including Rarity, Twilight, and Pinkie Pie. As they turn away to head to Rarity's shop, Pinkie stops and looks behind her in confusion just in time to see herself round the corner.

"Orphan Pink"

Concept/Synopsis: While in Manehattan with Rarity and Pinkie Pie, Twilight spots a second Pinkie, and finds out that not every Pinkie clone was sent back to the Mirror Pool.
Extra Details: This takes place directly after "A Study in Pinkie". The title is a reference to Orphan Black, a show about clones and the ethics of cloning. The episode will take on a much heavier tone than the previous episode.

Untitled Manehattan Cutie Mark Crusaders Episode

Concept/Synopsis: While visiting with Babs in Manehattan, the Cutie Mark Crusaders get the idea to check out their Manehattan branch, only to find that the filly in charge now is ruining what made the Crusaders so great in the first place!
Extra Details: This takes place directly after "A Study in Pinkie" and at the same time as "Orphan Pink". The episode will start with Rarity dropping the three off at Babs's place so they can go check on Rarity's Manehattan branch.

Untitled Fluttershy Episode

Flutterbat hanging from a tree branch S5E21

And this time, it's not just a costume.

Concept/Synopsis: When Starlight and Trixie's magic lessons go wrong, Fluttershy begins having strange dreams, her pets seem afraid of her, and to top it all off she always seems so tired no matter how much sleep she gets...
Extra Details: This takes place parallel to "A Study in Pinkie", "Orphan Pink", and Untitled Manehattan Cutie Mark Crusaders Episode. It is a sequel to "Bats!", bringing back Flutterbat. The solution from "Bats!" can not be used since it's now a result of a different magical mishap. The episode will start with Twilight and the others leaving for Manehattan.