This is one of my favorite pieces of fanart, if only for how emotionally charged it is.

Celestia looks somehow vulnerable in this one, which is very unusual– even though we have a lot of somber Celestia fanart (I think), she usually has her stately composure. This feels like an intensely private moment.
 
…I’d add that it’s entirely possible to be terrified of a benevolent, sweet, lawful-good person– if a disappointed look from them could break your heart; if you’d never forgive yourself for letting them down. Maybe Twilight just worships Princess Celestia a little too fervently.

Well wend you think about it like this.
 
Celestia is like twi’s second mother and she just moved out. Wouldn’t you freak out and clean out your place even if its pretty clean and you know she wouldn’t care much?
 
And well Twilight overreacting to minor stuff seems to be a trait of hers.

Oh, of course.
 
So instead of a complec and adorable psedo-mother-daughter relationship, we get Twilight being a simpering kiss-ass and poor Celestia trying her darndest to be a pal.
 
Which is almost as good, to be honest. So much unrequited friendship.

Actually, I was noting the anatomy of Celestia’s legs myself. They’re drawn as human legs, not equine legs. In a horse, the knee-equivalent is much higher up, the heel looks like a second knee, with the foot being the lower leg. I hope that makes some sort of sense.
 
Sadly, the person who wrote that first hug has, in fact, left MLP. The first two episodes were written by Lauren Faust.

Celestia’s hind legs are broken.

Maybe Twilight has a personality disorder like Aspergers or something that means she can’t discern emotions probably? (More likely that whoever was behind the hug died/had a stroke/was fired/went mad and thus Twilight’s view on Celestia changed.)

My personal headcannon? Everything we see in the show after the pilot is Twilight trying to “win back” Celestia after she feels like she was dismissed and then discarded in the pilot. Yes, to an outside observer, this makes not sense. Celestia clearly trusted Twilight to handle the rescue of her sister, and then was trying to make her favorite student happy by letting her stay with friends. But emotions don’t always make sense, and Twilight’s heart isn’t listening to what her head is telling it.

Or maybe, just maybe, seeing Twilight curled up in a little ball under her wing reminds Celestia of how Luna used to do that when she was young. And since this is obviously still before Twilight and friends freed Luna from her psychic prison, Tia is feeling both remorse at having to imprison her sister so many ages ago, and apprehension that maybe Twilight isn’t strong enough to defeat NMM when she appears.

Yeah, I only see her as someone who just makes what the unicorns used to do (move the sun) easier.
 
As for the Twilight thing… I want to say maybe she thinks the annoyingly nice part of Celly is mostly a facade.

Well, okay. I’m going to go ahead and headcanon this until we get further exposition: Twilight is very powerful, even as a filly. One day, she figured out how to grasp the sun, and tried moving it. If you believe that Celestia is the embodiment of the sun, or something similar, this could have been seen as a gross violation of her personal space, and would probably be one of those few things that could break her composure and really piss her off.
 
So, one thing leads to another, and as a result Twilight is terrified of the very notion of making Celestia mad, even if it was just one time and probably very brief. You don’t go around pissing off a goddess.
 
There has to be a good reason. Twilight fears what Celestia would to to her if she failed her. Ergo, Twilight is afraid of Celestia/ You don’t just fear a benevolent, sweet, lawful-good person for no reason.

Twi fears “failing” Celestia, not much Celestia herself.

When you think someone is going to exile you from your country forever just because you didn’t turn your homework in on time, you’re scared of them. Never mind the fact that Celestia has never done anything remotely cruel, except for maybe smashing Twilight’s heart during the finale. And to be honest, she kinda deserved it. There’s a right way and a wrong way to go about things.

I wouldn’t go that far.
 
Anyone can get paranoid by what’s more powerful than them. This is no exception.
 
Honestly, I forgot all about that hug.

I still have to agree with Lium. In the pilot, Twilight’s hug with Celly was absolutely heartwarming, and we haven’t seen any of that since. Instead, Twilight’s disposition towards Celestia has sort of done a 180, and she is instead more or less scared of her. Sure, Twi’s paranoid and neurotic, but you’d think she’d trust a pony who is practically her second mother a little more. Of course, you’re right, she doesn’t really get others’ emotions at all, else she’d treat Spike a lot better too.
 
But, no. The writers didn’t just drop the ball, they set it on fire, crucified it, and raped it. Then ate it.

she has brains, a fuck ton of brains but little to no understanding of emotions and how others think, i think that is a classic personality…

I wouldn’t call her ungrateful. But she’s kind of a dumbass. She probably is the closest friend Celly has, yet she thinks Fluttershy would go into a dungeon for taking a “malnourished” bird. Though, I think obliviousness to others’ emotions is consistent for her.

Yeah, true. And to be honest, she doesn’t seem all too grateful, either. If anypony has earned the right to call Celestia just Celestia and treat her as an equal, as a friend, it’s Twilight. And she’s possibly the most blind of them all.

Without Celestia, Twilight would probably be less of a kiss-ass, though.

Well, at least… Twilight wouldn’t be half the pony she is today if it hadn’t been for Celestia. She owes her success and talent and just about everything to her. I don’t think she’d be able to stay mad at her for long, if at all.

I’ll go for the 3rd (4th?) option and say she just remembered the ending of a sad movie she watched before.

Imp, both? and more?

Stabbed to death with feels.
 
Now, the question is: Is she crying because she’s getting heartbreaking feelings of deja-vu, or crying because she has carefully manipulated Twilight’s life so that she’d be able to save her sister, and feels awful about it?