Rurouni Kenshin: Meiji Kenkaku Romantan, Yu☆Gi☆Oh! 5D's Recommendations
Main Chars are similar in someway as they experience a tragic past only to haunt them. Both form friends whose resolve is to forge more bonds and in other words: friendship. The bad guys are alike though not exact. The stories in each show contain mature content that proves darker than other shonen series.