When I watched Magical Mystery Cure for the first god-knows-how-many times, there was a detail I failed to notice. Twilight suddenly knowing what to do and glowing was always weird to me, until I compared it with what happens to the remane five shortly afterwards.

Finding the Part of Themselves That's Been Lost

Reflecting Back on Past Experiences S3E13

"And they mean more to me than anything."

Fluttershy have a little snack S3E13

"Aww, look at that. I guess you were all just cranky because you were hungry."

Both Twilight and the Remane Five chose to try and help their friends, even if it's beyond their abilities to do so.

"My Friends!" / "My Destiny!"

Spike shields his eyes S03E13

"My friends!"

Fluttershy rediscovers her destiny S03E13

"I... I feel strange, like... like this is what I'm meant to do, like this is who I am! My destiny!"

Both Twilight and the Remane Five glow with a brilliant light. (BONUS: Twilight becomes the Princess of Friendship, meaning that, in a way, she also realizes her destiny here.)

The Epiphany

Twilight sparkly eyes S03E13

Downloading friendship problem solution, please stand by.

Fluttershy's Memories S3E13

Downloading Fluttershy, please stand by.

Both Twilight and the Remane Five have things appear in their eyes. (BONUS! Both culminate in something to do with cutie marks: Twilight's cutie mark appears in her own eyes, and the Remane Five's cutie marks reappear on their flanks.)