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This is the ultimate checklist for My Little Pony: Friendship is Magic, only applying to the Mane Six ponies. Here's the statistics for it as of mid-Season 7.

Twilight Sparkle Episodes with Applejack 1.png Look Before You Sleep
Episodes with Rarity 1.png
Episodes with Pinkie Pie 1.png Feeling Pinkie Keen
Episodes with Rainbow Dash 2.png Testing Testing 1, 2, 3
Top Bolt
Episodes with Fluttershy 1.png The Hooffields and McColts
Episodes with the Cutie Mark Crusaders 1.png Twilight Time
Episodes with other characters 3.png Discord: Three's a Crowd and What About Discord?
Starlight: No Second Prances
No. of Mane Six ponies where each of them and Twilight are the only two to appear in episodes 5.png

Pinkie Pie: Amending Fences
Fluttershy: The Hooffields and McColts
Rarity: Gauntlet of Fire
Rainbow Dash: Top Bolt
Applejack: The Perfect Pear (cameo)

Episodes where she is the only Mane Six pony to appear at all 3.png Hearts and Hooves Day (cameo)
Princess Spike
A Royal Problem
Pinkie Pie Episodes with Twilight Sparkle 1.png Feeling Pinkie Keen
Episodes with Rainbow Dash 2.png Griffon the Brush-Off
The Lost Treasure of Griffonstone
Episodes with Applejack 3.png Pinkie Apple Pie
Hearthbreakers
P.P.O.V. (Pony Point of View)
Episodes with Rarity 3.png The Gift of the Maud Pie
Spice Up Your Life
P.P.O.V. (Pony Point of View)
Episodes with Fluttershy 1.png Buckball Season
Episodes with the Cutie Mark Crusaders 0.png
Episodes with other characters 0.png Despite this, Starlight Glimmer did have big roles in Rock Solid Friendship.
No. of Mane Six ponies where each of them and Pinkie are the only two to appear in episodes 3.png

Twilight: Amending Fences
Rarity: The Gift of the Maud Pie
Fluttershy: Discordant Harmony (cameo)

By the way, "Treasure of Griffonstone" was mostly just Pinkie/RD and "Hearthbreakers" was mostly just Pinkie/AJ.

Episodes where she is the only Mane Six pony to appear at all 0.png
Rainbow Dash Episodes with Twilight Sparkle 2.png Testing Testing 1, 2, 3
Top Bolt
Episodes with Pinkie Pie 2.png Griffon the Brush-Off
The Lost Treasure of Griffonstone
Episodes with Applejack 2.png Fall Weather Friends
Buckball Season
Episodes with Rarity 2.png

Sonic Rainboom
Rarity Investigates!

Episodes with Fluttershy 1.png

Hurricane Fluttershy

Another possible candidate is Flutter Brutter.

Episodes with the Cutie Mark Crusaders 1.png

The Cart Before the Ponies

As with AJ and Rarity, this episode is really just a supporting role for Rainbow Dash.

Episodes with other characters 1.png Scootaloo: Parental Glideance
No. of Mane Six ponies where each of them and Rainbow Dash are the only two to appear in episodes 3.png

Rarity: Rarity Investigates!
Applejack: Brotherhooves Social
Twilight: Top Bolt

Episodes where she is the only Mane Six pony to appear at all 2.png Flight to the Finish
Parental Glideance
Applejack Episodes with Twilight Sparkle 1.png Look Before You Sleep
Episodes with Rainbow Dash 2.png Fall Weather Friends
Buckball Season
Episodes with Fluttershy 2.png Bats!
Viva Las Pegasus
Episodes with Pinkie Pie 3.png

Pinkie Apple Pie
Hearthbreakers
P.P.O.V. (Pony Point of View)

Episodes with Rarity (and nopony else) 4.png

Simple Ways
Made in Manehattan
Applejack's "Day" Off
Honest Apple

Episodes with the Cutie Mark Crusaders 1.png

The Cart Before the Ponies

As with RD and Rarity, this episode is really just a supporting role for Applejack.

Episodes with other characters 2.png Spike: Spike at Your Service
Apple Bloom: Somepony to Watch Over Me
No. of Mane Six ponies where each of them and Applejack are the only two to appear in episodes 3.png

Rarity: Sisterhooves Social
Rainbow Dash: Brotherhooves Social
Twilight: The Perfect Pear (cameo)

By the way, "Hearthbreakers" was mostly just Pinkie/AJ and "Viva Las Pegasus" was mostly just Fluttershy/AJ.

Episodes where she is the only Mane Six pony to appear at all 5.png Family Appreciation Day
Somepony to Watch Over Me
Leap of Faith
Appleoosa's Most Wanted
Where the Apple Lies
Rarity Episodes with Twilight Sparkle 1.png Look Before You Sleep
Episodes with Rainbow Dash 2.png Sonic Rainboom
Rarity Investigates!
Episodes with Fluttershy 1.png Green Isn't Your Color
Episodes with Applejack (and nopony else) 4.png

Simple Ways
Made in Manehattan
Applejack's "Day" Off
Honest Apple

Episodes with Pinkie Pie 3.png

The Gift of the Maud Pie
Spice Up Your Life
P.P.O.V. (Pony Point of View)

Episodes with the Cutie Mark Crusaders 1.png

The Cart Before the Ponies

As with RD and AJ, this episode is really just a supporting role for Rarity.

Episodes with other characters 4.png Spike: A Dog and Pony Show and Inspiration Manifestation
Sweetie Belle: Sisterhooves Social and Forever Filly
No. of Mane Six ponies where each of them and Rarity are the only two to appear in episodes 4.png

Applejack: Sisterhooves Social
Rainbow Dash: Rarity Investigates!
Pinkie Pie: The Gift of the Maud Pie
Twilight: Gauntlet of Fire

There was one Equestria Girls animated short that only had the EG counterparts of Fluttershy and Rarity in it.

Episodes where she is the only Mane Six pony to appear at all 1.png Forever Filly
Fluttershy Episodes with Twilight Sparkle 1.png The Hooffields and McColts
Episodes with Rarity 1.png Green Isn't Your Color
Episodes with Rainbow Dash 1.png Hurricane Fluttershy
Episodes with Applejack 2.png

Bats!
Viva Las Pegasus

Episodes with Pinkie Pie 1.png

Buckball Season

Episodes with the Cutie Mark Crusaders 1.png

Stare Master

After this episode, Fluttershy took no further part in any more CMC episodes.

Episodes with other characters 3.png All Discord: Keep Calm and Flutter On
Make New Friends but Keep Discord
Discordant Harmony
No. of Mane Six ponies where each of them and Fluttershy are the only two to appear in episodes 2.png

Twilight: The Hooffields and McColts
Pinkie: Discordant Harmony (cameo)

Episodes where she is the only Mane Six pony to appear at all 0.png

The checklist will change as soon as Season 7 continues.