Fluttershy as an anime nerd. This guy called it.

@Background Pony #5A3A  
A large part of the issue is the fact that we rarely hear Applejack call Fluttershy by name. She tends to call the others “Sugarcube” at one point or another, and with the limited interaction Fluttershy and Applejack had in the first three seasons, it was borderline as to whether or not they knew each other.
 
S4, on the other hand…there are a lot of interactions between the two, both deliberate and subtle, like Applejack falling over onto Fluttershy, as she laughed at Rarity’s ridiculous dress in Simple ways, Fluttershy hiding underneath Applejack during Pinkie Pride, and Applejack like about “that shy filly living out her dreams” in Filli Vanilli. Personally I like it.
 
(I always justified their lack of interaction, btw, to the fact that they live very far away from each other, on opposite sides of Ponyville.)

@Background Pony #AA31  
What would really enhance the second panel is some stray pink petals in the breeze.

@SeraphimDawn  
As mentioned in an earlier comment, there’s “Dragonshy” and the cold open of “Keep Calm and Flutter On”. It’s not much, but it’s some.

Yeah, there is like no interaction between Fluttershy and Applejack to this point.

Applejack also brought a whole cartload of Apples over to Fluttershy’s place in Swarm of the Century, without even knowing what she needed them for.

@Splinter17
 
Thisthisthisthisthis

You and me both sister.

@Splinter17  
*TwiDash

TwiDah is so 2012. AppleShy is best ship.  

@picklebrain
 
She was incredibly nice and understanding to Fluttershy throughout the episode Dragonshy (a lot moreso than Dash has ever been tbh)
 
After that…Well…She helped get beavers out of AJ’s farm.

Seriously does Applejack even talk to Fluttershy directly at any point? I can’t remember.

Rarity: It’s not that I like Spike-senpai or anything. B-baka!

The little white bubbles really sell it.

Just go for the harem ending.

Seriously though, these two have like…the least amount of on screen interaction…even less than rarity has with pinkie and dashy (at least on screen), and even less than rare has had with flutters these past 2 seasons (the lowest)
 
Which is sad cause they are surprisingly compatable

@Princess♠Molestia  
B-but Rarity-senpai must notice her.

@Princess♠Molestia
 
Rainbow dash is a baka

when will jon-senpai notice me  

NOPE! Just Rainbow-senpai