@Trahzo  
Twilight knew Moon Dancer better.

Bad hair is Twilight’s expertise and big eyebrows is Fluttershy’s then why wasn’t she in Moon Dancer’s episode?

@PonyPon  
Why would someone have an ability with eyebrows?

@orochijes  
Truth. LOL

Season 5: The season of eyebrows.

@Background Pony #ABCB  
Not to mention that, at least how I interpret what OP may be implying, Twilight has experience with trying to convince a rigid pony into changing her ways. And, Fluttershy has experience with being aware of how other ponies can effect the nature around them. Which, Tree Hugger may be well versed in.

I’d argue it’s both ability and experience, and that Twilight and Fluttershy are specifically paired here as a result of the solution requiring both of those things. I mean, Twilight has the experience (and knowledge) to know that figuring out the source of the problem will be the best course of action to solve it, but only Fluttershy has the abilities to collect the necessary information needs Twilight to act. Conversely, Fluttershy has the experience needed to show kindness and talk to an individual who is antagonistic to others (e.g., Discord), but only Twilight has the ability to force all the feuding family members to stop the conflict and listen while Fluttershy does so.

They were the only two that could fly back and forth quickly between two mountains. Dash would have just had them eating each other after a few minutes.

Interesting question, actually. May be…

With eyebrows?