A good attempt, but severely lacking.
First of all, there was no pre-loader. With no preloader, you cut out a lot of quality. People with slow internet will have troubles watching if the movie moves faster than it loads, so they probably didn't even bother watching it.
Second, we've all seen cut-scenes like this before. Yes, it looks good, I'll give you that; however, it seems more bland than when it was first thought of. Some new ideas would be great.
Third, the sprite quality was horrible. They did not look pleasing to the eye--they were very blurry, and the background, though not moving, seemed to look alive in its low quality.
You DO have, however, a good sense of cinematography. The music choices and graphic tone set a good mood of "sorrow" at the end.
However, it doesn't make sense that Mario and Luigi were fighting, randomly, just for Mario to go too far and kill his brother and regret it. Though, like I said, that end part was done smoothly (mood wise).
I hope to see more of your work in the future, and I do hope to see you improve in the future. If you nurture your talent for creating intense or un-intense moods, you can prevail.