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Bad Ass: Firefly's initial mental picture of Lady Blue Star...
Badass Bookworm: ...is crushed when it's revealed it was an accidental asswhooping and she's a complete nerd.
Bitch in Sheep's Clothing: Lady Blueblood, who makes her descendent from the original timeline look like a saint in comparison. When Blue Star is first appointed to Celestia's court, Blueblood attempts to take advantage of their similar-sounding names by claiming they're related. Once Blue Star makes clear that the two of them have very different priorities, Blueblood actively attempts to use the Royal Court to put an end to the changes Blue Star is trying to bring about to Equestria.
Courtroom Chapter: In Chapter 10, Blue Star has to convince Equestria's Royal Court that her reforms are, despite Lady Blueblood's claims, actually beneficial to Equestria.
Defeat Means Friendship: To show that there's no hard feelings between herself and Starswirl V as a result of their duel, Blue Star offers to sponsor Starswirl to Princess Celestia (partly to ensure the changes Starswirl brought to Equestria still occur), an act that causes Starswirl to genuinely respect Bluelight and form a genuine friendship with her over the years.
Doomed by Canon: In the prologue, we see Twilight reading a prophecy much like the one from the show's pilot. At the end of the prologue, we see a note from another Twilight Sparkle, saying that she did the best she could to improve things, and she hopes the Princesses will forgive her one day. And finally, in Chapter 1, the Twilight from the canon timeline gets Trapped in the Past and adopts the name Blue Star. It's not hard to figure out where things are going from there.
Dramatic Irony: “Celestia, listen to me. Twilight Sparkle is not Blue Star.”
Expy: Each of the G1 ponies serves as these to Twilight's friends. She does notice some differences though, such as Surprise being slightly more levelheaded than Pinkie Pie, Posey being more likely to stutter than run in fear of another pony, and Firefly being more disciplined than Rainbow Dash. Sparkler, on the other hoof, is almost a perfect match of Rarity.
Ironic in that Twilight's friends are themselves expies of the G1 ponies.
Meanwhile, G1 Applejack is the silly pony you'd expect her to be.
Fan Nickname: In order to differentiate the original Twilight that time traveled from the one in the new timeline, the readerbase occasionally refers to Original Twilight/Blue Star as Bluelight.
Fantastic Racism: In the past, only Unicorns are allowed to read. Pegasi and Earth Ponies are forbidden to even enter a library. Bluelight seeks to rectify this.
Gambit Pileup: The story seems to be heading in this direction, with Celestia manipulating events to create the perfect bearers for the Elements of Harmony, herself being unknowingly manipulated by Luna to that very same effect, and the Order of Stars having its own, yet unspecified, agenda.
Giving Radio to the Romans: Blue Star brought numerous technological advances to Equestria from 1000 years in the future, and went even farther than that, actually doing a lot of further building on them within the past, beyond what had been accomplished in her native time. Ironically, one of the results was a stable time-viewing spell, which would have allowed her to avoid the whole situation if it had been around in the original timeline.
Heroic Sacrifice: It is heavily implied by her surviving notes, that Twilight took the Nightmare into herself to prevent it corrupting Luna.
In Spite of a Nail: For all the social changes Blue Star brought about (not to mention Luna's continued presence as a leader of Equestria), the world still developed very similarly, with Twilight still becoming Celestia's student, Shining Armor still developing a crush on Cadance, and so forth. Word of God is that this is an inherent trait of timeline changes in his version of the universe: The timeline tries to stay as static as possible, and pushes probability around to do so; therefore, any change which can actually have a longterm effect on the timeline has to be big. Luckily, the Order of Stars has been continuing Blue Star's legacy, preventing her improvements from getting canceled out by the timeline.
In Their Own Image: Blue Star pulls off a non-evil example; she advances society by hundreds of years worth of progress in just five years (with help from the Order of Stars to keep things going after she gets banished), leading to a far more egalitarian and technologically advanced future than the one she came from. In the process, she becomes pretty much the most famous historical figure we've seen in the new timeline.
Meanwhile, in the Future: The story alternates each chapter between Blue Star!Twilight in the past and Neo-Twilight and Trixie's friendshipping adventures in the new future.
Mood Whiplash: Most of Chapter 6 is a giant Heartwarming Moment covering Trixie's first Hearth's Warming with Twilight's family. Then at the end of the chapter, she recieves Nightmare Moon's helmet from the original timeline.
Mugging the Monster: Firefly's mental image of Bluelight after hearing the truth about the magical duel's outcome.
Firefly (inner thoughts): She was the young filly that got attacked by foolish muggers in the alleyway, assuming her to be an easy mark, only to leave them broken and aching by the side of the road. No, Blue Star wasn’t at all what she expected. She was better.
Subverted: Turns out that they were founded by Bluelight just before her Face-Heel Turn and have actually been responsible for some of Equestria's post-Darklight Star improvements. Bright Eyes herself confirms to Celestia that the Order has no intention of helping Darklight Star once she is released.
Retroactive Precognition: Blue Star knows everything that's supposed to have been done by Starswirl V before she accidentally usurped his Court position and sets out to make all the same accomplishments, and more. Meanwhile, in the Future the "more" is clearly evident.
Schedule Slip: Chapter 11 was scheduled to be published after Christmas 2012 was over... it is still unfinished as of Christmas 2013.
Tricked Out Time: Accidentally take somepony's position in history while Trapped in the Past? Use that power to endorse all their accomplishments so they happen anyway and then help make them better with futuretech.
WAFF: One of the major features of the Twilight/Trixie chapters.
What Year Is This?: Blue Star asks Surprise the year near the end of their first conversation. Surprise being herself, she doesn't find it an odd question at all.