See, I know I’m SUPER late to this discussion but I have a headcanon about this :3
Unicorns with magic-based talents have magic colors based on their cutiemarks. Meanwhile unicorns who aren’t magic focused have eye color based auras.
Twilight and Shining Armor both have pink magic, as Twilight’s talent is magic in general, whilst Shining Armor’s is protection magic. They both have the pink stars in their cutiemarks, which is where their aura colors come from. Starlight’s talent is also magic, so her magic aura is taken from the cyan magic swirls in her cutiemark. Sunburst’s talent is the knowledge of magic, which is still a form of magic-based talent, so he gets his yellow colored magic from the beams in his cutiemark.
Meanwhile Sweetie Belle has green magic and green eyes, because her talent is helping ponies with their talents. Her cutiemark has zero green within it, because it uses the pinks from each of the CMC’s manes. Trixie’s comes from her eyes, too, because her stage magic doesn’t require knowing hardcore spells. Flim and Flam have bright green magic that matches their eyes because apples aren’t known to symbolize magic within Equestria 😭
Of course there’s gonna be outliers, like Rarity! Oh.. Wait, her talent is sort of magic related.. That’s why her aura is taken from the lighter blue gems in her cutiemark, not the dark blue of her eyes! Her talent is gem magic, that’s how she earned her cutiemark as a filly and why she’s amazing with finding gems as an adult. She’s got a lesser magic talent, but it’s magic related nonetheless!
Please let me know what you think of this, as it’s honestly one of my favorite partially-backed-by-canon headcanons I have! I love talking about this subject so much!