If you liked the MegaMan NT Warrior manga, the Anime-Planet community thinks you'd like:
Misaki Suzuhara is a young girl who traveled to Tokyo to live with a relative, but ended up becoming involved in the greatest game of all time: Angelic Layer! In this fast-paced competition, players customize dolls and fight them in arenas of all sizes, hoping to gain experience and perhaps win the greatest tournament of them all! With new friends to meet and new enemies to defeat, the best time of Misaki's life seems to be just beginning. Join Misaki as she struggles to be the best, even in the face of overwhelming odds.
Both of these mangas revolve around a game in which the player controls the actions of his or her technological avatar. In Megaman NT Warrior, netops advise and aid their netnavis, who are sentient computer programs. In Angelic Layer, a deus sends telepathic commands to a robotic angel. If you enjoy scifi battle games, try out these two!
Reiji Ozora, a high-school student who excels at nothing, tires of every game he's played - that is, until one day his friend Maiko introduces him to the world of Dragon Drive. In it, players are given virtual dragons to ride and fight against one another; though unfortunately for Reiji, he's assigned to a small dragon with unknown attributes. Determined to increase his skills, Reiji soon jacks in to a training program when suddenly he, Maiko, and a boy named Daisuke are transported into another world called Riyku! In this new foreign land, not only must these friends try to find their way home and fulfill what is asked of them, but Reiji must also discover the truth behind his dragon's abilities.
In both of these mangas, kids start playing a game that turns into much more. Each kid has a partner that they use to fight other teams- in one manga, it's personal programs that interact with the net for them, and in the other, it's a dragon with unique attacks. If you liked one, you should check out the other too.