A mix of everything like we'd like to see more...
The first seconds were excellant, with impressive art of the protagonists. The logo in 3D with Swift3D was quite good, you know how to handle it ( even if i'm sure you can do even better with ).
Then everything seems a little "random", you present Bowser quickly, then you'll change with Sonic... Seems a little weird. Then the others ennemies... I think it would have been better to show them one by one, and not to cut it. It would be more impressive, you see, they are "bad" after all :)
Still, one thing was totally incredible : how can you make a sprite movie like this ? I mean... It's not a sprite movie anymore ! Well, it feels like. I really though i was watching an opening. Awesome.
The song you took was catching, and rocked your movie.
Well, if it was a little less 'random', it would have been almost perfect ( perfection doesn't exist XD ). Still, all in all, the little things you added, and the global charism of you flash movie were something i'd like to see more. There, all of you who are reading this, you can NOT deny that this serie has something others do not have. And you can totally see it, when you look at the intro.
And for that only, this intro was what you can expect from the author. This is more than enjoyable.