That's pretty harsh, I know, but it's true. You force people to download 13mb when they come on to your site. Your home page should be one of the smallest pages, because that's the first one people see. If they lag and have trouble with it, they'll leave.
As for the video itself. It's a great video (mostly) but it's done completely wrong. Firstly, you should NEVER embed video in to a Flash animation, unless it calls for it specifically. It makes it look unprofessional, and increases the file size DRAMATICALLY. That whole animation on your home page should be no more than 500kb at the max.
Some of the 3D effects are pretty cool, but mixing them up with normal video breaks the flow. You shouldn't intermix them >_<. Then there is the text. Times New Roman... *choke, gasp*. Not even any effects on the text.... that's terrible. Everything else looks pretty cool, but the text is just terrible.
Okay, enough crapping on about it. Here is my recommendations:
First, the text. Get rid of it. At least use something like white bolded Arial with a horizontal blur. And some nice transition effects on the text would be good, like a fade in, or make it fly in from the side!
As for the movies flow, here is what I would do. Get rid of all the interlaid videos, clear them all out for now. Focus on the flash animation and those trippy 3D effects. Have a nice short opening sequence of just Flash animation, with a few text scenes in the middle. Then at the end, have a nice big title page. Then, have the title page fade out to a selection page with a few short videos of your scanner. So a few big buttons, click the button and the screen loads the video and displays it. After it runs through it, it goes back to the selection page.
So essentially, it'll be an opening Flash animation then a choice to load some short videos of the scanner in action. It doesn't have to be complicated like youtube or anything. Make the videos in flv format and have them dynamically loaded in on demand. No controls, once it is loaded it covers the screen and plays.
Again, yes, that is pretty harsh. But this is the work I do for a living, it's my job. So expect it to be my honest, professional opinion