Watching how similar but different Twilight and Sci-Twilight are as characters. They both share the same Adorkable nature but their nurture led to them having different personalities, particularly the latter being a Shrinking Violet.
For starters, both were The Ace in their worlds. However, Twilight's case was better because she excelled at magic, which is Serious Business in Equestria, leading to her having high self-esteem. On the other hand, Sci-Twilight only excelled at academics and this led to Intelligence Equals Isolation as a result of jealous peers, leading to her having a low opinion of herself. Secondly, Sci-Twilight doesn't have the local Big Good as her personal mentor. Whatever one may think of Celestia's Trickster Mentor behavior, the influence of Principal Cinch was definitely worse for Sci-Twilight's development.
Seeing all the flack that the human Twilight got from her peers just because she was the top student, you can't help but wonder if the Pony Twilight we've spent the last five seasons getting to know and love went through similar experiences. According to one major fan theory, it would explain most of her antisocial attitude in the pilot and factor into her low self esteem...Remember the horror of "Magic Kindergarden"?
Twilight almost completely ignoring Flash Sentry, even after he helps her and is nice to her. Heck, Derpy has to comfort the poor guy after Twilight brushes him off. And even though Sunset and the Humane Five are well aware of his crush on Twilight, none of them bother to inform him that this is the Twilight from the human world, so he thinks Twilight lost interest in him.
"What More is Out There?" While the song has its hopeful moments, it's basically Twilight singing about how she's an outcast at Crystal Prep and despite all of her achievements, she still feels like something is missing from her life.
Perhaps the saddest lyrics are "maybe I'm better off alone/will I find what I'm looking for, if I just do it on my own?" Knowing how important friendship is to this and the main Equestria, it's kind of crushing to know she's basically given up on ever having friends.
The original version was a Distant Duet with Sunset Shimmer and it is available in a deleted scene. She talks about her homesickness for Equestria and that alone is pretty sad but it is more complex than that. Unlike Sci-Twilight, who looks forward to the great unknown, Sunset knows for a fact that there is "more out there" because she has seen it and has since been separate from it. She has no idea what to do with herself and wonders if someone, somewhere in the world, needs her help.
Twilight's reaction to Cinch dangling her application into the independent study group she wanted to get into in order to make her compete in the Games, all in a plan to increase Cinch's own reputation.
The novelization outright states that Twilight's main reason for wanting to go to Everton is to escape Crystal Prep. Literally, that's what's written in the book, twice.
[When Lemon Zestshares her headphones with Twilight on the bus] She closed her eyes and thought about her independent study. She could endure this. She had to. It was her only way out of Crystal Prep — and she had to get out. [During the archery competition, against Applejack] Twilight looked into the stands and caught a glimpse of Principal Cinch staring at her. She couldn't lose her chance to get into Everton. She couldn't. It was the only way she would ever escape Crystal Prep.
Twilight is trying her best to hit the target in archery but keeps failing. She's about ready to burst into tears while her teammates get more and more frustrated with her. It's so bad that Applejack steps in to help her, even though it will hurt CHS's chances of winning.
Anyone who suffers from extreme anxiety when under pressure in this sort of situation (read: being watched by an entire audience, your team mates berating your efforts, and you being responsible for falling behind) can really relate to Twilight in this. Just seeing her start to cry really does hit home for those who've been in her shoes.
If Spike being able to talk is Nightmare Fuel for Twilight (however briefly), it qualifies as this from Spike's perspective: your best friend, your caretaker, your family that has been with you, if not for most of your life, then a good part of it, is suddendly running away in absolute fright from you — and you do not understand why.
Sunset venting all of her frustration at not being able to understand magic at Human Twilight. The fact that she has a point, that Twilight should not be messing with things she doesn't understand and putting herself and others in danger, makes it worse.
As for Sunset herself, once Rainbow Dash helps her calm down, she immediately wishes she could take her entire outburst back. On top of that, Principal Cinch begins throwing accusations that Canterlot High is using magic to cheat in the games, something Sunset not only promised she would prevent, but is also responsible for bringing to the school in the first place. Even though no one blames her for these things, it's not hard to imagine Sunset feeling like the biggest screw-up in the world at this point.
From Twilight's perspective, not only has she, even if by accident, endangered the lives of the competitors and possibly the spectators, but gets a severe chewing out by a complete stranger that's absolutely in the right. And what Sunset tells her...
Sunset Shimmer: You're supposed to be so smart, but did you ever think you shouldn't be messing around with things you don't understand?! Twilight Sparkle: But I wanna understand! Sunset Shimmer: But you don't! And worst of all, you put the lives of my friends in danger! Twilight: I didn't mean to! (runs away in tears)
Once again, the novelization gives a more detailed look into Twilight's head. Namely, her sheer confusion and pain after the same girls who were nice to her just a few moments ago were now yelling at her (well, Sunset is).
Twilight's transformation into Midnight Sparkle. Having the human counterpart of a character many fell in love with over the years painfully transform into a demonic creature, who only desires to understand magic at the cost of destroying her own world, can be heart-wrenching to witness.
When Spike is trying to reach Twilight before she release the magic in the amulet during the song. His "Twilight, no!" just cinches it.
Imagine what Spike's feeling during the scene. He is witnessing the person he loves the most in the world transform into a demonic Mad Scientist determined to understand magic, even at the cost of destroying their universe. No wonder Twilight temporarily regains her sanity when she sees Spike looking up at her. For a moment, Twilight can see what she's become in her only friend's eyes.
Her tearful "Help me!" before she gets fully sucked in followed by desperately reaching out for someone to pull her out was also exceedingly hard to watch.
Remember: This is a girl in high school. She's like 15-17 years old. She's still just a kid. Now, watch her transform into Midnight Sparkle, and keep that in mind.
When Sunset tries to tell Midnight that her machinations are destroying the world, the latter merely snaps So what?" This can be interpreted as Lack of Empathy. Or it could something very sobering: that Midnight Sparkle is a manifestation of how sick Twilight is, not just of Crystal Prep, but of our world, an uncaring world that bullied her and neglected her. It makes one very uneasy to imagine Midnight Sparkle doesn't care about our world, even when there's still good people in it. Thank goodness Sunset reminds her there is such thing as the hand of friendship.
Sunset Shimmer comforting Midnight Sparkle in the magic white void. The fact that Midnight Sparkle looked so frightened, until she took Sunset's hand.
During the final event of the Academic Decathlon, Sunset and Twilight compete to solve a difficult math problem. Sunset gets the answer wrong and thus loses. That in itself might count for this very briefly, as she's clearly disappointed because she believes she let everyone down — but her friends hurry to her and shower her with praises and affectionate gestures, as she got the Canterlot Wondercolts the closest ever to victory. Meanwhile? Twilight's teammates-slash-classmates don't even smile at her for actually winning, greeting her with only half-hearted clapping, and Twilight can only look at Sunset and company sharing a group hug. Hidden by her chalk board, she turns away and sighs. She looks lonely, and it shows just how terrible things are for her at Crystal Prep — she's not loved, liked or praised by her uncaring classmates and Principal even when she gives them just what they wanted.
While they are bonding over their love for pets, Fluttershy points out to Twilight that even if the latter won, her team barely was ecstatic. Twilight somberly explains that no one in the Crystal Prep cares about anything they didn't do themselves.
In a blink-and-you-miss moment, right before the start of the finals, Sunset is seen with a confident smirk, while her classmates are rooting for her. But Human Twilight? She lowers her head in anxiety, but has literally no one who support her in the background.
