The Heart: Works to keep everypony on track, and tries to help both Twilight and Trixie learn about Friendship.
Pay Evil unto Evil: Justifies stealing by claiming she's never taken anything from anypony who didn't deserve it. Bear in mind she says this right before swiping a merchant's clothes for calling her a thief.
Beloved princess of Canterlot Castle, she has a hypnotizing grace few ponies can resist...
A Taste of Power/Early-Bird Cameo: Not Celestia herself, but her treasured Esper Stone, Unicorn, which lets her, Luna, Twilight, and Trixie potentially learn all of its spells before Espers are properly introduced later on.
Jack of All Stats: Early on, she's noticably less squishy than Twilight and can fight just as well as she can cast magic.
No Indoor Voice: She starts off using her ROYAL CANTERLOT VOICE! all the time, save for an aside to Tia. However, after encountering Fluttershy, she learns how to dial it back in a somewhat familiar fashion for normal conversations, busting it back out whenever appropriate.
Fluttershy as Shadow (F-Shy)
Delicate and demure with the sweetest little voice, but be careful, or else she'll give you... THE STARE!
Acrophobic Pegasus: The only pegasus who can't Soar, due to having The Stare instead. To compensate for this, when she first joins the party, she's carrying a Pony Feather which lets her float in battle.
Shrinking Violet: So much so she can't stand up against the reputation her Stare has brought her.
Trixie Lulamoon as Celes Chere (Trixie)
Once Great and Powerful, now fallen from grace. Her biggest obstacle in life is her own ego...
Dark Magican Girl: Unlike Celes in the orginal game, Trixie can't use many of the swords that Celes can and instead limited to staffs and daggers early on, relegating her to this rather then a Magic Knight. (On the other hand her Runic... er Unicorn, command can be used with any weapon since she uses her horn)
Shadow Archetype: While Twilight was enslaved by the Empire due to her natural magical talents, Trixie willingly joined them in order to be infused with her powers, and is extremely proud of her abilities.
Shock and Awe: While originally An Ice Pony like Celes, as of v0.95 she now learns the Bolt family naturally rather than Ice.
A precocious pink party pony who loves making others smile, even when she has nothing to smile about herself...
The Berserker: Notably Averted; unlike Gau, Pinkie usually doesn't fall out of the player's control after selecting a Random attack. (The exceptions being when the selected moveset includes automatically casting Berserk on herself, such as Brawler).
Gameplay and Story Segregation: Casts Ice magic in a cutscene before joining the party, but doesn't know any Ice spells when she first joins. (While she does know a Water/Wind Blue Magic attack, she doesn't name it when casting in that scene.)
Carrying the Antidote: After your first battle with him, he drops a Harmony Band, which blocks the very same status effects he kept casting during the fight.
Darker and Edgier: Though some of his dialogue is certainly still amusing, his general demeanor is surprisingly more serious than Kefka's or even his own canonical appearance on the show, giving rather straightforward dialogue in lieu of some of Kefka's more memorable one-liners.
Off Model: His sprites for his battles in Neigshe and the final boss fight are clearly mirrored versions photoshopped out of screenshots on the show. As a result, his arms appear to be on the "wrong" sides.
Gilda Griffon as Emperor Gestahl
Famous Last Words - Et Tu, Brute?: Her reaction to Discord's betrayal is rather sad, as it implies her realization that there is no one left on her side in the end. "Not...You...too?"
A Mother to her Stallions: Like General Leo, she shows far more respect for her Mooks than other Imperial Commanders and chews one of her subordinates out for being so hasty to dive into a dangerous situation.