you need some work...
This flash wasn't a bad effort. But if you're going to improve you're going to need a lot more than unfounded compliments. So I intend to offer some constructive criticism.
First off, the animation needs a lot of work. I understand you're new at animating, but still the fact remains. The animation was anything but fluid, and the fact that this is a sprite animation, where you don't have to draw every individual pose, doesn't help. Try to make the animation a lot less simplified and choppy, and at least consider making some new sprite poses that go along with the action. I'd rather watch a thirty second animation that flowed smoothly than a longer animation that's choppy. Likewise, it was interesting to see so many enemies, but this was watered down by the lackluster ways in which Mario defeats them. I'd rather see a well put together fight with one enemy than a hundred bland fights. Do you get what I'm saying?
Along the lines of sound, the music is good, but as you said it is the work of someone else. I will at least credit you for find a tune so suitable to this type of animation though. It'd be nice if this wasn't the only sound in the video though. Some well timed sound effects would increase the impact of the animation. Sound effects can be found just about anywhere on the internet, and are easy to download.
As to the story, it was a nice idea. Mario fights a whole bunch of enemies, but is finally overwhelmed by Bowser. It works, in a way. But to me what doesn't work is that Mario gets all the way up there, and then runs away. there's no real explanation for why he wanted to get up there in the first place. And when he just suddenly gets a cape and flies off, it makes me feel like you got tired of animating and wanted to end it already.
Now I do want to compliment you on the creativity of using the germs. The idea of them coming out and literally infecting Mario was interesting. Then I had to laugh when Mario pulls that "Green Mile" stunt and blows the germs out at the koopa kids. I'm not sure if you wanted that to be a gag, but that's how it came across.
My final synopsis is that if you want to make sprite animations, you're going to have to put a lot more effort into this. And sure I know most people would say that three months is a long time. And maybe you're satisfied with this as the finished product. But if you're not satisfied, then my advice is put a lot more time and effort into it next time, and you might have something impressive.