SSB4 with characters: [u'Mewtwo', u'Samus']
Similar issue to Mega Man but less prominent. Mewtwo can reflect a lot of projectiles Samus uses, making it near impossible to hit a Mewtwo that has good timing.
SSB4 with characters: [u'Mega Man', u'Mewtwo']
As a player of both Mewtwo and Mega Man, I can safely say that I think that Mewtwo would win this fight, simply due to the fact that most of Mega Man's attacks can be Confused and thus reflect back at Mega Man. Granted, a good Mega Man should be used to being attacked by his own projectiles (which is pretty sad) but it is still a very hard matchup.