To be honest, I never liked Super Mario for a couple of reasons: it has a short amount of hits that you can take before you die (1-2), there are limited checkpoints per level (or none, my memory fails me), and it gives you a limited amount of hearts (3 for the entirety of the game) which if you lose all, you have to start all over. Those things might not be as bad separately, but combined together, they make the game harder and unpleasant to some players.
Mega Man on the other hand, addresses some of these issues by adding a life bar that allows you more hits before you die and it provides you with health packs that replenish it. Also, different enemies inflict different amount of damage, which can be used do add variety in the world and different levels of difficulty on different parts of the level. Another things Mega Man has that Mario doesn't is all the different weapons that you can use to your advantage and make the game more pleasant. The variety of weapons also helps in the development of divergent and more unique levels, with parts that can only be accessed with the use of specific weapons (e.g. blocks that can only break with a hyper bomb explosion.)
Even though Mega Man has those things developed in a better way than Mario, it is still a game that I wouldn't play because of the limited amount of checkpoints on some levels as well as the moderate to high difficulty of the game that make it annoying to me (probably even more annoying than Dark Souls.) This might be because I haven't played the original game and levels, where the balance of checkpoints and enemies, as well as the overall level design are probably greater.
P.S. I don't know why other people say that the controls of the Mega Man Maker port are bad. I thought they were fine and I don't think that there are a lot of other ways they can be implemented more suitably on a keyboard.
