The development of the story is very intense for them and they have a beautiful happy ending.
They weren't born as couple, or as lovers, they're just "the safe and the saviour", because Aoshi saved Misao when she was a child and helped her to become strong, in order to live in an difficult epoch like the one of the Meiji period. Misao growed up with a big admiration for Aoshi, an admiration that day by day will become a deep love for her! But Aoshi didn't love Misao, she's important for him but like a little sister or a friend. Also, Misao's feelings for him are very deep and I think that in the bottom of his heart, Aoshi proves the same thing for her! Misao is a little girl, she's delicate but not weak, her tecniques of fighting are strong and she uses them mostly to prove that she can protect her beloved person. Aoshi uses ninja tecniques and teached them to Misao! So she's very proud of her fighting style and she will fight forever with kunai and other ninja arms. Her relation with Aoshi is sweet but a bit sad...
He wants to protect her and she wants to protect him but for different reasons, and the most important one is Misao's love. She thought that Aoshi won't ever return her feelings, and many times he rejected her, but she never gave up.
Her feelings are unbreakable and sincere, and going on along the series, he had to change his mind! The Oniwabanshu team is the proof that they're made to stay together, since Misao and Aoshi share the same goal: protect Kyoto and the Shogun! Misao's determination to stay beside him was so strong that Aoshi couldn't stop her, even if her life was in danger. He always protected her and she risked her life for him, definitely, they share the same feelings but in a different way. Aoshi won't admit how she's important for him but in his heart there's a place that only Misao can take. And the same thing is for her, he's the only one that she always loved and followed, for any reason she would betray him, and at the end of the story they're togheter because their bond made them inseparable!!! I'd really like to take care of their fanlisting, they're characters I love very very much, the sweetest relationship in Kenshin's series and in the major part of shounen manga too!