Excellent concept, but...
Something of this calibur is simply amazing. The fact that you went and made this at all is by itself phenomenal; recreating the entire Mushroom Kingdom is enough of a feat, but then coding six somewhat different characters to play through it? Truly a great idea.
However, the game itself is quite flawed. I've seen it mentioned that some of the characters have low jumps. I encountered this with Simon, with whom I only played once, then gave up; after all, if his standard jump can't clear a low pipe in a game that's supposed to be all about jumping, then he shouldn't be included. I understand the idea is to have him use the double-jump, but there are times when that is really difficult to pull off.
The biggest gripe I have, however, is the powerups. Aside from Mario, they do NOTHING but provide your character with another hit or two before they are killed. I played mostly as Megaman, probably because the games he is in are so similar to those of Mario. I'm willing to agree to enemies taking a few hits to kill with the normal Mega Buster; giving one-shot kills with a primary projectile weapon would make the game all too easy. Might as well give Mario fireballs right off the bat if you're gonna do that. However, when he powers up, the impact of his hits seem... less than rewarding. I got pretty stuck on Map 4-1, and while there, I noticed that the Spikies seemed to take four hits to kill normally, but three to kill with the charged Mega Buster. Alright, that's fine. But then I got the Fire Flower... STILL three hits to kill a Spiky. I'd think that, at one's most powerful, regardless of who they are, if they're in a Mario game and have the strongest power-up in the game, everything should be killed in one hit. Having me launch three of my strongest attacks to kill an enemy when my second-strongest attack could do the same thing is ludicrous.
Also, Lakitu's a bitch to kill. Not really a valid point, just an opinion; it felt like I shot him, like, 9 times as the Contra guy and he would not go down.
Overall, it seems like you did a good job on everything except the powerups. It's probably easily fixable, so if you develop a version 2 of this game, I hope that that gets on the list of things to improve.