Exactly what I was thinking... 2 hours of Flash?
Even for 30 min of playing time, I wouldn't like to be your computer's battery!
Well, it's Adobe we're talking about here so...
I have rendered 3 minutes, frame by frame, in Maya for 10 hours straight, it was a nightmare.

I was surprised the MacBook Pro didn't turn off on me. It got SO LOUD and was scorching hot!
Of course I wouldn't do that in Flash. HTML5 would be even worse though.
After Effects is more emphasized in the digital video courses though, the only time I used it was when I had to put all those Maya rendered out images and make a few changes before I saved it out.
The animation course in my college is more about learning to structure your work with storyboards, learning to use Photoshop, Illustrator, Indesign, and the basics of Flash. And then of course using Maya to render and animate. The smaller certificate anyway, the main one has you do math and writing that focus on liberal arts.
They'd rather us take improvisation, theatre, and dance than a HTML course. They are more beneficial and will help you do better work.
You're learning how to tell stories, and how to put them in art form. HTML5 is cool, but you'd draw it all out and finalize it before even bothering to even start doing it. And at that point, you probably have it in a program already, so why not use that instead?
Like someone else said, it doesn't matter what you do it in, it just has to be in the correct exported format.

But I like sticking to Adobe stuff because it's what I know. It would be like going from Maya to Blender.
Oh and a strong portfolio and basic HTML (that is in good taste), is better than a weak portfolio and good HTML.