Hurricane Fluttershy (S2)
While this episode is more about Fluttershy getting the confidence to fly in an important tornado, Rainbow Dash also has a subplot of desiring to break a world record. The best scene was definitely when Rainbow first comes over to Fluttershy’s place. After Shy reminds Dash how she used to be teased, Dash at first angrily tries to tell Shy to suck it up, but stops herself and calmly tells Shy that she needs every Pegasus she can get. At one point, despite being told that they could break the record, Dash was still worried about Shy. Yeah, this is THE episode for the two Pegasi in the Mane 6.
Other Nominees: Dragonshy (S2), Trade Ya (S4), Tanks for the Memories (S5)

Putting your Hoof Down (S2)/Filli Vanilli (S4)
Noticed how I didn’t bold these episodes? No matter where I look, I can’t find an episode where the focus is on Fluttershy and Pinkie Pie. I did say I’d fill the spot with an episode where the two ponies interact with each other a lot, even if the focus is not on them. Anyway, why I’d chosen Putting Your Hoof Down: Despite it being an episode focusing on Fluttershy taking assertive lessons too far, Pinkie (along with Rarity) acts like the straight mare, giving advice to Fluttershy. As for Filli Vanilli: Throughout this episode, Pinkie keeps insensitively worrying Fluttershy about how everyone would silently criticize her. Until, an episode comes where the focus is definitely on Fluttershy and Pinkie, these two episodes are the runner-ups to this category.
Other Nominees: None others

Green Isn’t Your Color (S1)
This episode is the one most focused on Rarity and Fluttershy. Rarity gets jealous when Fluttershy gets a modeling job instead of her, though Rarity tries to support her by insisting Fluttershy does the job. Fluttershy actually hates being a model, but continues to do it because of Rarity’s insisting. Both confine in Twilight how they really feel, but eventually admit their feelings about it to each other. So yeah, these two Beauties of the Mane 6 have this episode as “their” episode.
Other Nominees: Putting Your Hoof Down (S2), Castle-Mania (S4), Filli Vanilli (S4),

Bats! (S4)
Despite the unbalanced argument between the Mane ponies, this episode clearly has Fluttershy and Applejack in the spotlight. Applejack wants to get rid of the Vampire Fruit Bats; Fluttershy wants to allow the bats to have a section of the orchard; a disaster occurred; A.J. swallows her pride and goes with Fluttershy’s solution. Despite the reception of this episode, this episode is currently the only episode that clearly stars Fluttershy and Applejack.
Other Nominees: None others

Bird in the Hoof (S1)/Hooffields and McColts (S5)
For the longest time, I’d considered Bird in the Hoof to be the episode where Twilight and Fluttershy are the focus of the episode. However, Twilight is only with Fluttershy within the 1st and 3rd acts of the episode. Only now in Season 5’s Hoofields and McColts do they stick together throughout the entire episode.
Other Nominees: Keep Calm and Flutter On (S3),