MapleStory is doing just this with an upcoming patch. In the second chapter of the Black Heaven storyline, players will be able to jump into a flying machine and duke it out in the sky. As with everything else in the game, the action will take place strictly in a side-scrolling 2-D format. From the looks of it, it calls back to classic shmups of earlier console generations.
Also coming in one of the future updates is a revamp to MapleStory's Resistance classes, including the Wild Hunter, Battle Mage, and Mechanic.