I hate being a tough critic but . . .
This sprite animation has some good points and bad points. I, being the harsh critic I am, mention more of the bad points, but I mean well.
When "Evil Link" first appears, I think a "shadow link" sprite, or just a darker color scheme in general, would have worked to show Evil Link's difference.
Luigi inexplicably has lightning abilities. He was pretty much Raiden in this homage to Mortal Kombat. Also, one of his lightning strikes was aimed relatively low, and Luigi somehow throws him into it. I can also mention that it's lightning, so the speed at which it travels would be considerably fast.
For some strange reason, Mario wound up around the Castle. Even stranger, the first room Luigi checks is the bathroom (idc if he's a plumber, they really never plumb). The strangest part is that there's no door . . . for your bathroom . . . I understand if the house was made that way, but Luigi could have had the decency to give a warning before barging in on him.
Idc about power levels (since Mario would only be able to take to hits anyways), but Naruto has become almost a cheap sprite with his clones. Whether or not he wins, his clones, who all do the same damage as the original before separation (meaning they all somehow have the same amount of chakra), repeatedly beat or get beaten easily. I'd, personally, like to see Naruto's clones used more like what they do in the manga (the anime is slow at times . . . so a few turn pages is faster in my opinion).
In this series, Mario is a horrible, immoral person. It's not his castle, and they're not inside the castle; Naruto just happens to be there, and Mario jumps to conclusions and decides to fight him. He also throws in the first punch, instigating the fight. After losing, Mario lies to Luigi, saying Naruto attacked him for no reason. Whether or not this was done on purpose, Naruto could have either avoided the fight (due to his speed) or defended himself. It's outside his personality, and seemed more like a Sasuke thing to just let it go.
Of course, considering my suggestions would turn most of these dialogues, realizations, encounters, and fights into a turn for the worst. I just wanted to mention some of this stuff so you can improve, not to belittle. I always enjoy watching sprites and sprite clashes. Unfortunately, this means that this idea isn't original, but hopefully, with your resourceful imagination, you can think of a great, long-lasting story that's worth watching.
The music was really great to listen. Hearing the sound effect, "GET THE F*CK OVER HERE!" is always a treat to the ears, whether or not you're against cursing. The homage to MK, the addition of the Mario universe, Zelda universe (although it should be Link since he's actually in all his games), the Naruto universe, and the other universes (idk who E. Gadd is, or where the background sprites come from, sorry) mesh well together. I really do enjoy the fact that you actually put mario and luigi in there, and that they could fight, a feat that proves difficult in flash animations. I hope you can improve on this, because this may not be perfect, but it's nowhere near garbage (hence, my 5/10). Good job, keep up the great work! ^.^