Sora is pretty strong. Even after losing all of his skills in Chain of Memories he still beat Guard Armor and a member of the Organization. Marth has okay skills but Sora just has more. Sora can make lightning, blizzard, fire, and he has summon cards. Sora wins.

Update 2/7/2019 thanks to Fire Emblem Warriors Marth is strong and fast enough where he can turn the tides of battle and win. Marth wins.