I didn't really get it... but good work, I guess!
The thing with this Flash was that it didn't really seem to serve any distinct purpose. It's story was short, it's humor was lacking in some departments, and the overall presentation was below average.
Also, I didn't quite understand why Mario and Sonic weren't mortal enemies.
But the Mario Music alone makes it worthwhile watching in my books. A few pieces of advice for a sequel:
1. Have the text appearing in a black box beneath the Flash. It makes it easier to read.
2. Make it longer, include more random games references etc.
3. Try to develop the story further.
Overall though, good effort, good achievement.
TBO