Still there are two things that would still make me pick Flash as the technology of choice and I don't like that, so we should fix it!
Fullscreen is awesome. Even Steve Jobs thinks so. I personally think we should do something really simple to fix this:
window.openalready has all the security restrictions in place that we expect from a modern browser with a built in popup blocker. There might need to be extra restrictions with respect to keyboard events (so that pressing ESC always takes you back) but even not having keyboard events at all would be fine for a start.
2. Ease of Deployment
The deployment story for Flash is awesome. Send someone a SWF file, he can play it. Yes, for more advanced use cases the file might reference a couple XML files and other asset and might need some parameters to get going but overall that's it.
If you haven't worked in big multi-Agency projects (which would be a good thing :) you might not appreciate this point as important but it really makes sense to have an exchange format for content which one can just "drop" into what is already there.