If there is one thing that tends to be asked about this shipping, it's "Why?". Why Subaru and Luna? He should be with Misora! Or what about Tsukasa? Well, not everybody agrees with that. Misora-wise, she's the "Roll" of the series, is she not? Even though Megaman/Rockman has usually been paired with Roll in the later, please remember Roll was originally Rockman's sister. Tsukasa, not everybody is a fan of yaoi or shounen-ai, despite the fact that he may seem genderless, there are places that say he's a male.
For those who don't ship Subaru with Misora on the sole fact that she's the new "Roll", it's because she's the other female in the series and because of Luna's craziness in the anime. Due to the anime coming out before the game, even though the game was in production first, most people just saw the anime and originally thought "Wow, Misora and Subaru are great together!" because the anime killed a lot of Luna's personality.
So, what makes Luna and Subaru so special? Because, they have learned from eachother. Subaru learned what it was like to protect someone, to care, when he promised to protect Luna and Luna sensed his bravery and his caring, even before she was sure he was Megaman, because he promised he'd protect her and she felt that, both as himself, and the hero. Once he became friends with Luna, Subaru started to smile more and it was Luna's efforts that really got him to school, even if she tricked him a bit. They do bump heads a bit, but at the same time, they go together just as well, because they bring a sense of unique-ness and understanding, and Megaman or not, Subaru was who Luna began to confide in, and that's what makes it so special.