Rurouni Kenshii

Rurouni Kenshii by IncandescentKitsune is basically a Gender Flip treated like a For Want of a Nail scenario, with Kenshin being born female (not exactly the biggest stretch) and dubbed Kenshii. Oddly, s/he isn't the person who the most unlike their canon counterpart, but Enishi, who ends up as being not crazy. And a protagonist. And not crazy. And not a villain. Did we mention not crazy?

Sadly, while the concept is surprisingly intriguing and the first few chapters are quite good, it isn't any longer than that; it's both very short and most likely dead.

Tropes used in Rurouni Kenshii include:

Arranged Marriage: Kaoru wonders if this is why Kenshii puts up with Enishi (who she perceives as just a Jerkass). At least until she finds out that, we ll...
Belligerent Sexual Tension: Kaoru and Enishi.
Bratty Half-Pint: Enishi was this, by his own admission.
Curb Stomp Battle: Both of Kenshii's fights.
Dead Older Sister: Tomoe.
Deadpan Snarker: Enishi, to Kaoru's great annoyance.
Driven to Suicide: Implied to be the case with Tomoe.
Embarrassing Nickname: *snick* Eni-chan. *snort*
Face Fault: Enishi does this in the first Omake when he hears Kaoru's Relative Error. Kenshii's reaction is similarly shocked.
Foe Yay:

Kenshii: Though personally, I always thought at least some of the rest of the Shinsengumi figured it out, what with the way some of them were always sort of flirting…

For Want of a Nail: Despite Kenshin being the one who was gender flipped, Enishi went through the most significant change, going from a crazed, psychotic Big Bad to a protagonist. Had the fic gotten far enough, the last manga arc probably wouldn't have happened. At the same time, smaller changes are scattered about, such as Kenshii's outfit not being the trademark pink and Tomoe being buried in Tokyo instead of Kyoto.
Gender Flip: The premise and the nail.
In Spite of a Nail: Kenshii still has the trademark scar despite never meeting Tomoe, Enishi still uses wattoujutsu, the same swordstyle as he did in the series, and Tomoe is still dead.
I Resemble That Remark:

"Don't call me stick girl!" Kaoru shouted at him.
"Don't pick on Kenshii!" he shouted back. "Just because she's too nice and puts up with your mood swings…"
Kaoru stuck her tongue out at him, before brightening and turning to Kenshii, proving Enishi's point.

I Was Beaten by a Girl: Since the dreaded Battousai is a woman, this comes up a lot.
My Greatest Failure: Enishi blames himself for losing Tomoe...
My Greatest Second Chance: ...And hopes to help Kenshii when he couldn't help his sister.
Noodle Incident: One of the six people who knew Kenshii's true gender during the war was Saitou, “though he was an accident.” And that's all they say about it.
Only I Can Kill Her: Intentionally invoked when Kenshii has Enishi learn wattoujutsu so that if her Super-Powered Evil Side ever did take over, he could kill her.
Pass the Popcorn: When Kenshii takes over a fight from Enishi, he continues to watch nearby, anticipating the thugs inevitable Mass "Oh Crap" moment when a woman half their size makes them eat dirt.
Platonic Life Partners: Kenshii and Enishi, though there also doesn't seem to be anyone else in their lives (their loved ones have this tendency to end up missing, estranged, or d e ad)
"The Reason You Suck" Speech: Enishi gives one to Kaoru when she accuses him of being Battousai and trying to attack him. Because attacking someone you think is a murderer in the dead of night with a stick is a good idea. He gives her another one when she attacks someone she knows to be a murderer with a broken stick. Kaoru isn't amused.
Relative Error: Kenshii and Enishi are essentially Like Brother and Sister. But since anyone could tell they're not related by blood and appear to be around the same age, Kaoru (and who knows how many others) assumes they're married.
Replacement Goldfish: Kenshii is this in relation to Tomoe, as she takes the same role in Enishi's life and he admits to how similar the two are.
Shipper on Deck: Kenshii is quick to point out how alike Kaoru and Enishi are, despite protests.

Enishi: (After Karou takes over cussing out a police officer) I take it back, I like her.
Kenshii: See! I knew you'd like her given enough time – you're too similar not to like each other…
Enishi: We are not similar!
Kenshii: Of course not, Eni-chan.

Shout-Out: The name Kenshii was originally used in “Samurai X”, the Sony/Columbia dub of the show.
Sweet Polly Oliver: Kenshii pretended to be male while she was fighting in the revolution, but has gotten too old to pull it off anymore.