A Crown of Stars: In this story Shinji has a degree on Philosophy and Asuka another on Advanced Mathematics. Shinji's time studying Philosophy often comes up, and Asuka has been seen reading up on Mathematics.
The Child of Love: Asuka is mainly a fighter and a warrior, but she is also a fourteen-years-old genius with a college degree. In chapter 7 she could not sortie to fight a giant alien, but she contributed with her strategic expertise and thanks to her tactics her teammates managed to win that battle.
Evangelion 303: Asuka is a commander of the USAF and an elite pilot of experimental jet fighters. Her profession demands not only being a great fighter but also studying a lot, as seen here.
HERZ: Shinji is an Humongous Mecha pilot -and he has been one for the past twelve years- and a music teacher.
In Sotto Voce: Impa is a warrior who likes to read. Zelda notes that this is a rare trait.
Last Child of Krypton: In this story Shinji is Superman. He also knows German and it is implied that he reads about a wide variety of subjects.
Chasing the Shadow has Sakura, an average twelve year old girl managing to keep up with the most gifted kids of their generation through sheer brains and guts
Albus Dumbledore, as per canon. He's a brilliant wizard, a master of magical theory and alchemy, as well as being conversant on Tony Stark levels in the hard sciences, as well as having a generally broad knowledge base. Fighting wise? In the first book, he takes down four witches and wizards handpicked and trained by HYDRA specifically to take him down, with about two spells (and a third to destroy their wands), while absently analysing their casting styles and deducing their origins, and with half his attention elsewhere. In the second book, he's faced with an Eldritch Abomination that was a god-killing low-level Reality Warper to begin with, one that then possessed a teenager who was technically an Omega-Class Reality Warper twice over. He didn't just fight it - he mopped the floor with it.
Hermione is academically brilliant, with a mind that Loki noted for its potential - and which turns out to be so well organised it has its own filing system. As for fighting, she isn't a fighter by nature, but shouldn't be crossed - for one thing, she's the strongest natural chaos magic practitioner since the Scarlet Witch (which given that she's Wanda's daughter, isn't surprising) and in the sequel, an Omega Class mutant. For another, she's got a ruthless streak, a cool head, and she's perfectly handy with both wanded and wandless magic, with the sequel revealing that she's been methodically mastering how to wandlessly cast every wanded spell she knows. Oh, and that's without using chaos magic.
Victor Von Doom - skilled statesman, capable strategist, designer and builder of his own Powered Armour (which is emphatically not a copy of Iron Man, beyond the basic shared physics), and a brilliant and exceptionally powerful sorcerer capable of dismembering multiple powerful master vampires.
Magneto - scientist with multiple degrees in the hard sciences, multi-lingual (he went from basic English phrases to fluency in a matter of months), and designed and built a modular space station 3/4 the size of Hogwarts that only needed outside help on the life-support systems. He's also an excellent teacher. Oh, and he's an Omega Class mutant capable of manipulating electromagnetism, power mastered through his scientific knowledge, and he's a deadly Nazi hunter.
Doctor Strange, who epitomises 'knowledge equals power'. As Dresden notes, he's learned from history's magical all-stars via time-travel (and via a vastly extended lifespan, has had all the time in the world to do it), and in multiple realms at that. His raw magical power doesn't actually exceed Dresden's, which is formidable, but still mortal, and below the likes of Wanda. He's also capable of duelling Physical God and Eldritch Abomination level opponents into the dirt, and his precision is ridiculous - if he wants to, he can split atoms. He's also an excellent teacher, when he bothers, one of the greatest bards ever to live as a hobby, and a legendarily skilled medical doctor who can cure wounds to the soul and effortlessly whip up an infertility cure. And that's all aside from his ability to manipulate everyone, ever.
In Legionnaire, Twilight Sparkle turns into one of these over the course of getting trained by The Equestrian Legion for her mission to Tarhen.
The Second Try has Shinji and Asuka becoming milder examples of this trope by necessity, since they had to accumulate and learn the sum total of human knowledge after they're left being the only two humans left alive on Earth, and are pigeonholed into being a civilization of two.
In Tails of the Old Republic, Miles "Tails" Prower of Sonic the Hedgehog fame is now 14 years old, up from his canonical age of 8, and he can both kick ass and take names in Star Wars: Knights of the Old Republic. When it's not trying to kill him, the technology he's surrounded with makes him drool like a kid at a candy store.
In the Pokémon story Brave New World, the first new addition to Team Aurabolt is a fat basement-dweller Squirtle with tenuous grasp on thedifference between fiction and reality. He starts things off by pounding the crap out of the protagonist (who has already defeated entire armies) via Confusion Fu, proceeds to predict half the plot turns in the story, defeats homicidal demons via children's card games and a manifestation of the futility of life using nothing but logic, stores entire arsenals in his shell, holds his own in direct combat, and generally embodies Crazy-Prepared.
The fic Mortality shows what happens if you really get a mild-mannered doctor like Watson seriouslypissed off. It's NOT pretty. If you really manage to get him pissed, this mild-mannered doctor WILL calmly kill you.
Tara "Green Shield" Strong from DC Nation. Yes, she is a Snark Knight first and foremost, but this is someone who has a Masters at 19, is getting her M.D. by apprenticing under Doctor Mid-Nite, and got her abilities by playing Professor Guinea Pig on herself to try and prevent her crooked boss from taking credit for her work. She's even studying alchemy in order to better keep up with the magical trouble the JSA attracts.
John in With Strings Attached qualifies. In Real Life he was a voracious reader, and a songwriting genius. In Strings, he's transformed into a guy who can fly and lift half a ton (though not at the same time) and given a magical charm that makes him powerful enough to lift a river. Not that he actually wants to do anything to you—unless you fuck with him or the others.
Paul and George probably qualify as well.
Harry in Harry Potter And The Invincible Technomage. Not only is he on his way towards being as brilliant as his adopted father Tony, he also gets regular physical training from Hell by Captain America.
In The Age of Wings and Steel, Cranberry uses her knowledge of ancient history to save the team's quest in the north.
The Pony POV Series has Twilight Sparkle, of course, but there's also Dark World Spike, who's spent the last thousand years as Discord's slave doing pretty much nothing but read to pass the time, from which he's learned a number of fighting techniques.
Harmony Theory: Star Fall is a scholar, magic talent, spy and powerful (by modern standards) mage, able to use her abilities in a fight.
Starr from Pokéumans, despite being seen often in her dorm reading, has certain moments of awesome. The best of which being when they infiltrate Pokextinction's Pine Barrows base.
Princess Luna, from Nightmares Are Tragic and All The Way Back, is one of the two strongest Alicorns in Equestria, a highly-skilled mage and mistress of numerous weapons and fighting styles. She is also extremely knowledgeable in science, technology, history and the arts.
The Celestia Code features Twilight Sparkle again, as an alicorn. Her approach to dragon negotiation is step 1, offer barter; step 2, carefully applied violence. She also uses applied topography to change a spherical magical shield into a buzzsaw.
In Equestria Girls: Friendship Souls it's been repeatedly pointed out that warrior's greatest weapon is their mind and creativity. True to that, people that are scientist and schoolars are dangerous and some can even fight opponents above their power level:
Clover. Member of the 12th Division and able to take on a horde of Hollows alone.
Twilight Sparkle, she's capable of fighting opponents stronger than her, using her wits and magic, and is smart enough to design and create artificial limbs. Then she became a Sternitter.
Captain Starswirl. Captain of the 12th Division and head of Soul Society's R&D, and perfectly capable of slaughtering countless foes with all manner of reisatsu-based chemical compounds created by his zanpakuto.
Discord. Former Captain of the 12 Division, creator of the Hogyoku, and more than capable of training Sunset even after the latter has achieved Bankai.
Cave Story Versus I M Meen stars Jack as quite possibly the most Badass Adorable fanfiction character ever, with incredible durability and persistence, a healthy balance of brains and brawn, and even the abilty to use ZA WARUDO.
Thousand Shinji: Shinji and Asuka take pride in both their fighting skills and their intellect. Even though Shinji is capable of beating almost anyone in physical combat, he considers his brain is his best weapon. And Asuka is thirteen and she already went to college.
Shinji: I presume then that you want me to help you with your written Japanese. Asuka: If you could. I can help you with your homework, I took most of it already when I was in college. Shinji: (squeaking because she's thirteen) You went to college? Asuka: Yeah, I graduated last year. Shinji: Do you want to lose your virginity tonight? Because I am so turned on right now. Brains, beauty, and a degree in what I must presume is ass kicking, what more could a guy want?
Yin and Yang Series: Fujuju seems like a quiet, bookish guy at first... only to end up being a dangerous pyromaniac.
Twice Upon an Age: Victoria, Dorian, and Cullen all fall into this category in All This Sh*t is Twice as Weird. All three are highly skilled in battle, and are also voracious readers with particular interest in history. It forms a Commonality Connection for all of them.
Robb Returns: Rodrik Harlaw, nuncle to Theon and Asha Greyjoy, proves himself as this. His epithet may be "the Reader", but he is perfectly capable of leading the forces of his more militaristic goodbrother Victorian Greyjoy into a trap, as well as beating the man himself in single combat.
The Pieces Lie Where They Fell: Page Turner might be a librarian (in fact, helping another colt find the book he wanted is how she got her Cutie Mark), but you don't want to mess with her in a fight.
Infinity Train: Blossoming Trail: In contrast to how the anime portrays her, Chloe Cerise is an avid reader of books and skilled enough with a steel piper (or "donut holer" as she calls it) to knock someone off their high horse.
Cronus: Hermione beats up Cormac after he tries to gang-rape her, then kicks him in the crotch as the finale.
Boldores And Boomsticks: Shade, Blake's Gastly/Haunter, spends most of his free time reading. He still put up a good fight against Guzma's unusually strong Golisopod before the fight was prematurely ended by a ring out.
Harry and the Shipgirls: The destroyer Fubuki studied the tactics used by multiple navies during World War II and used them to literally write the book on shipgirl combat tactics. She's also capable of winning a slugging match with a Battleship Princess.
My Choices: Twisted Tales Through Time: Firefly's initial mental picture of Blue Star as a hardened warmage is crushed when it's revealed that the incident that created this impression was an accidental asswhooping and that she's a complete nerd who loves reading and magic theory. It turns into this after a few sentences from Blue Star about why she shouldn't learn to properly fight, since her power is so great that she could easily hurt her opponents by mistake.
: Japan is very smart. He can also match Germany in combat despite being a full six inches shorter and much thinner.