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Mirai Nikki certainly has fun with this trope. Almost immediately after stumbling into The Game, Yukiteru encounters Yuno Gasai, a beautiful girl in his class who makes it her top priority to protect him from harm (and does pretty damn well, to boot). The catch? She's batshitfrickin'insane, and at even her most "sane" moments likes to break into his house or send him hundreds of emails over the course of an hour.
Miu from Kenichi: The Mightiest Disciple. Kenichi repeatedly vows to protect her, despite the fact that she's still a more skilled fighter than he is. Eventually he comes close and has actively protected her several times when she was sick or disabled. Still, her Grandfather won't let him date her unless he can beat him in a fight. Said Grandfather is an Old Master.
Tokiko in Busou Renkin is this to ordinary high school guy Kazuki Muto - the series starts out with her resurrecting him from the dead after he got killed on the spot by one of the series' "homunculus" (evil demon things) and later kills the creature. She becomes Kazuki's mentor, and a little later becomes severely weakened due to a parasitic demon-infested probe, with Kazuki saving her life. He eventually surpasses her in power.
A good half of Yuuto's Unwanted Harem in Omamori Himari qualify, though Himari herself is the most obvious example. Yuuto himself has yet to actually fight, though he has the potential to equal or surpass all of the girls when he finishes his training.
The Pandoras and Limiters' relationship from Freezing could count.
Merry to Yumeji from Yumekui Merry could count; according to Isana, Merry does indeed like Yumeji, she just isn't fully aware of it.
Although they're a Battle Couple too, girlfriend Ramona Flowers does end up fighting some enemies that boyfriend Scott Pilgrim doesn't have the balls to (those enemies being women), something both of which Ramona and his enemies call him out for being a pussy on.
Anyone who shacks up with Wonder Woman is going to fall into this trope, save maybe for Superman or Batman. Steve Trevor, Wonder Woman's golden age whipping boy, was a World War II U.S. intelligence officer, but couldn't exactly hold his own against Greek gods, sorceresses, or several hundred feet tall women.
DC Comics also has Big Barda and Mr. Miracle, two New Gods from the planet Apokolips. While Mr. Miracle isn't a pushover (the man regularly escaped deathtraps designed by Darkseid), Barda used to run the Female Furies, an all-female Apokoliptan strike team. Oh, and she's canonically almost as strong as Superman.
As seen below, Fox to Wesley in Wanted. Portrayed differently in the comics, where the characters are DC supervillain pastiches, and Fox is quite clearly Halle Berry cosplaying Catwoman, sent by Wesley's not-quite-dead father to make a man out of the geek.
Ludmilla Leonovna, in David Weber's The Apocalypse Troll, fits this trope to an extent, though as with Leeloo (above), her male love interest was a bad-ass himself before they met — a U.S. Navy captain who rose to that rank through the SEAL teams. It's just that she's an immortalSuper Soldier from The Future...
Most female Wizards from the The Dresden Files - special mention to Elaine and Warden Commander Luccio, both for the protagonist.
Also for Harry, badass cop Karrin Murphy and reporter Susan Rodriguez, after she's turned into a proto-vampire.
Kitai, of Codex Alera. In. Freaking. Spades. Only in the finale could Tavi possibly match her in direct badassery, except that he's her totem animal and they mutually gain power through that bond.
Any female character, really. If she's important enough to be included by name, she can hold her own against 99% of the populace in raw furycraft or swordswomanship.
This is a general trend in Jim Butcher's books - he's very gender-blind in assigning badassness, and many of his main characters have plausible romances with at least one other main character.
Percy Jackson and the Olympians: Annabeth to Percy in the first book, as she's been training for years while he's only just discovered he's a demigod and relies mostly on his natural powers. By the time they actually get together, he's more than caught up and is a Bad Ass all of his own. He's still happy to admit there are some areas, particularly battle strategy, where she's more skilled than him.
Kahlan Amnell of the Sword of Truth, especially before Richard learns how to properly use his sword and magic. After that, they're more of a Battle Couple She's also much better at tactics, even though he's more inspiring and has a better grasp of strategy.
Others' fear of Kahlan's power prevented her from developing any sort of relationship, including romantic ones. Richard fell for her before he knew how dangerous she was, and she was very surprised that he didn't care.
Cara to General Benjamin, forming a very heartwarming Battle Couple.
Nicci, first to Jagang (for very squicky values of "relationship"), and later, unrequited to Richard.
Special mention to Egwene, Nynaeve, and many of the Green Ajah who are in love with their Warders, forming many a Battle Couple.
Elayne, Aviendha, and Min would be this if their boyfriend wasn't the Dragon Reborn, the series's designated badass. It's not even a polygamous Battle Couple, it's entirely possible that he's a physical incarnation of the Creator himself.
Tuon for Mat. She looks like a pampered doll, but she's had combat training and faced assassination attempts since she was little. All her really extravagant clothes have loose pants and a tunic underneath it. The last three books are her slowly realizing that she's the Battle Couple variant of this trope.
Birgitte Silverbow, in a reincarnating Battle Couple with Gaidal Cain, though she's by far the better known of the couple.
The younger version of Mary Winchester from Supernatural would count as this trope, since it was revealed that she used to be a hunter herself even before John had learned about the existence of monsters and demons.
Spartacus: Blood and Sand: When Sura was being attacked and Spartacus shows up and starts killing her attackers, does she run and hide? Hell no! She picks up a sword and kills one herself!
Doctor Who: Rory might be the Whoniverse's resident Badass, but he doesn't exactly like the adventurous lifestyle. His wife Amy is far more gung ho about going on adventures. She even saved Rory's life several times.
In the same vein, River Song, the aforementioned couple's daughter and eventual wife of the Doctor is certainly more actiony compared to the main protagonist. While the Doctor would solve problems with his brains, River would solve them with some feminine charm and a gun.
Tengaar from Suikoden I. She and her boyfriend Hix live in a town with a very rich warrior culture. He doesn't like fighting, but she's more than determined to "make a man out of him".
Princess Sapphire. Although Almaz is certainly no slouch in combat ability, its clearly obvious that Sapphire is the stronger warrior. It should be noted however that Sapphire's primary affinity (based on stats and evilities) is towards ranged combat while Almaz is a close combat fighter.
Depending on the boyfriend - it's a dating sim - Hiyoko of Hatoful Boyfriend can be this or half of a Battle Couple. In the first game there's little chance to explore this, but in the second she makes up for that and repeatedly acts the bruiser for her less vigorously athletic male companions.
In Girly, officer Hipbone is this to Policeguy when he's not fighting too. An old opponent faced him when he had retired from the force (and thus couldn't get into fights without ending up in trouble), so she fought for him. The guy tried to mock him for this, but Policeguy just sat back and enjoyed the show.
Whateley Universe example: Bladedancer. Gateway and Chain Lightning may both have mutant powers, but they're both having to step up their game to be the significant other of the Handmaid of the Tao.