Much has been said about the absurdity of her genius and the amount of suspension of disbelief required to take her seriously. We won’t rehash that argument today.
Her Harley Quin personality is a matter of personal taste. Again, not the key issue, despite it being a fond target for folks who simply dislike her.
In literature, the literary element conflict is an inherent incompatibility between the objectives of two or more characters or forces… The literary purpose of conflict is to create tension in the story, making readers more interested by leaving them uncertain which of the characters or forces will prevail.
— Wikipedia on Conflict (narrative)
Herein lies the true problem.
What exactly is Scarlet’s objective?
We. Still. Don’t. Know.
Without this clarity, we do not have any CONFLICT.
Without conflict, there is no tension. No suspense. And no damn interest in the story.
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Players cannot oppose Scarlet’s objectives if we don’t know what she’s up to. We can’t be the villain to her hero (or vice versa) if we have no clue as to her motivations.
We have to stop her! Apparently.
From doing what though? Dunno. Graffiting the landscape? Wait and see, I guess.
And she’s certainly not opposing us, is she?
Despite being supposedly set up as the villain of the Living Story.
After all, who exactly is the protagonist of the Living Story?
Is it us, the players?
We began with pretty much no objective. Our destiny was to be fighting dragons and we defeated Zhaitan (but stupidly forgot to burn or even check on the body.) On to the next dragon, right?
Mysterious things happen and our objective becomes find out what is going on. Obstacles set up in our path mostly involve wading through a sea of red names with no real setbacks and collecting a drip feed of information as the writers felt like giving them to us. Certainly, Scarlet wasn’t actively preventing us from finding out what was going on. She just stands around giggling, being mysterious and telling us it’s all going to plan, toodle-loo.
Somewhere along the line, most players’ objectives have converted to catch and beat the hell out of Scarlet and her minions because they’re bloody annoying.
While admittedly she remains elusive, thanks to deus ex Arenanet, players have been galloping along a wave of success with very little ups-and-downs (innumerable Molten facilities trashed, clone armies of Aetherblades farmed, Queen assassination attempt foiled, more rustbuckets left lying in pieces, giant krait tower strewn about the landscape in even more massive pieces, etc.)
Scarlet’s visible successes appears to be several new factions-of-the-month, a dead Lion’s Arch councilor whom we’d never heard of (promptly replaced by another), the removal of Faren’s clothing, and some homeless quaggans.

We cannot suffer a story setback if we have no clue what she’s gotten away with. She could be building a giant molten toxic twisted steam dragon golem airship in her super-secret base in the Mists for all we know.
After all, she’s gotten away with murder and graduating from three Asuran colleges. In her backstory. Behind-the-scenes. Read the website, thanks.
But without visible setbacks, there is no perceived threat or tension to the storyline.
Nor are we really uncertain which of the characters or forces will prevail here, right?
Game-wise, the player is bound to prevail eventually.
Story-wise, she -could- prevail, except we don’t even know what she’s prevailing over. We’re reaching the end of the story and we still have no bloody clue.
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The best villains are those we can empathize with, almost get into their skin and understand. Their motivations are clear.
They may go about achieving their objective using very questionable means, which morally, the heroes are bound to oppose, but most don’t go about what they do for shits and giggles. They have a compelling need to do what they do.
Magneto believes the war of humans vs mutants is inevitable, and that homo superior will eventually win. He’s just hastening the process and defending his kind.
Hannibal Lecter is a super-intelligent and urbane sociopath who likes the taste of human flesh and doesn’t have moral compunctions against ridding the world of stupid and rude people.
To bring it back to Guild Wars examples, Vizier Khilbron sank an entire nation. Why? To stop the charr invasion. For his god and for power and eternal lichdom.
As for his god, Abaddon, well, nevermind that he’s a murdering psychopath, he’s been -betrayed- and -backstabbed- by those dirty Five Human Gods and chucked into a plane of eternal Torment, so -of course- he wants revenge.
Minister Caudecus is wise and beloved by his supporters, especially among the nobility. He’s just politically opposed to Queen Jennah’s decisions and enough of a human supremacist to prefer dealing with cutthroat bandits than with charr.
Ajax Anvilburn, on the other hand, is a charr supremacist who can’t let go of the war either.
Kudu is researching Elder Dragons. Important research that can’t be disrupted or delayed for such minor things like moral qualms regarding the use of lesser species to accumulate further knowledge.
Mad King Thorn wants OUT. (And a joke that kills you.)
Bloody Prince Thorn wants OUT and to show daddy who’s boss.
Scarlet has no such motivation made clear, beyond apparently keeping one step ahead of the players and laughing at them. Her primary purpose appears to be trolling people. We call that a childish griefer, not a compelling villain.
Oh, and fusing seemingly random things together, I suppose. For research purposes. Because this somehow holds the key to… what? Leylines of magical energy? Did she get cheated by Zommoros once upon a time? Did she fuse her brain with an asura?
Maybe she found some really good weed when she looked into the Eternal Alchemy.