While Fluttershy is ultimately the more motherly type, Applejack is ultimately the one who leads the team around when Twilight is either unable to lead or she believes she shouldn’t lead. I don’t want to bring up this for a point, but notice how Applejack told the others to check on (fake) Cadance and they all complied without a second thought and how she’s the only one who actually apologized to Twilight. Not to mention that she’s the one who suggested Twilight goes back to her Princess duties.
She’s the first pony Twilight formally met, the first Pony to activate her Element, and the first Pony to fall to Discord’s temptations. And for good reason. She’s practically the moral ground that the others stand on. Without her, they just crumble apart.