If you're looking for manga similar to The Legend of Zelda: Phantom Hourglass, you might like these titles.
A boy named Enta is invited to come to the Battle Frontier by Scott. Once there, Enta decides to battle each of the Frontier Brains.
Yuu Shirogane is a hot blooded school boy who competitively plays the Nintendo DS game Pokemon Platinum in order to become the Battle King.
Britannia's seas are being ravaged by monsters under the command of the sorcerer Vitor, head of Magincia's merchants. The young pirate captain Susadora and his gang - accompanied by Rani Sentri, captain of Britannia's special forces - are commanded by Lord British to find arms strong enough to stop Vitor, as well as discover a mysterious truth about Susadora himself.
Hareta is a young boy with an ability to communicate with Pokemon. He's lived the past few years in the forest near Professor Rowan's lab, but now a new adventure awaits. Along with the Professor's assistant Mitsumi, Hareta is sent forth on a mission: find the legendary Pokemon Dialga, a creature with the ability to control time! The road there will not be easy, but Professor Rowan gives Hareta a Pokedex filled with Pokemon info to assist him on his quest, and a feisty bird named Piplup accompanies him to fight by his side. Together, the new friends travel from town to town, gaining experience, getting stronger and finding new Pokemon along the way. However, dark secrets, fierce challengers and an evil organization known as Team Galactic stand in their way!
Who says pirates can only be cutthroats and bloodthirsty pagans? Meet Kid, the world's most notorious pirate and womanizer, and his rowdy crew that consists of not only pirates but also a priest and a mermaid?!
Alamos Town: home of the world's largest musical instrument, hot air balloons, and the newest Pokemon contest. Ash, Brock and Dawn have travelled to Alamos Town to take place in the battle, and with the help of a local guide named Alice, the gang and their Pokemon explore the city. However, danger awaits: the immensely powerful Dialga and Palkia are having an epic battle in the folds of space time, and soon their destruction will spread to Alamos Town itself. Meanwhile, a mysterious Pokemon known as Darkrai - known for causing nightmares - has surfaced. What is the connection behind these events, and can the city be saved?