"A good flash for when you're bored"
I had trouble getting into the flash to begin with. Even though it was loaded the main menu didn't show up. I think I reopened the window twice before it decided to work. I've got no idea what the problem was.
Your main menu looked dull. It needs a background like your scene select had. Scene select menu was really good by the way. That skip to percent thing was something I've never seen before.
Anyway I should talk about the movie...
The start begins rather boring with Luigi finding a mysterious machine but it's only quick and there's a lot of nice camera movement to keep a viewer's attention.
The next scene with Donkey Kong was also boring and also slow with little movement but I understand you needed that part for story development. I think you were using the character's sounds to fill in the gap and make the scene more interesting but it really needed movement. Donkey Kong's stand cycle was close but having the character's jump or something when they say an important line would really make the scene easier to watch.
Link's scenes were the best. I actually laughed a bit when the ship was on Link's dad. One thing I have to congratulate you on is the "many hours later" part. I'm so glad you decided to pan over to it instead of the "blank screen with text" approach. Little things like that really help the quality of your flash.
The animation on Luigi's word bubbles was nice. It was odd having to click on his bubbles though and not having to click on Donkey's which were automatic. I really don't know why you did it that way. I would suggest taking out the flashing arrow as idiots like me think they have to click on the arrow every time instead of just the bubble which is much easier. Last bit about text bubbles, be careful with what colours you use, the purple on black was getting a little hard to read.
Also take out the custom cursor. Normal cursors are so much easier and work better.
Animation and sound were fine. They weren't special (sprites never are) mostly you sticking to what the actual games are like with in-game sounds and sprites. I suppose there's nothing wrong with that it's just nothing new is all.
All up it was a good flash for when you're bored.