Interesting thread. After reading it through, i must concur on having the EXE or APP wrapper. HTML 5 is great and all for developing playable game on any platform, granted if the browser supports it. But not entirely sure how this would benefit game developers who would want to market and distribute their games if was only in the HTML 5 format. On the Chrome App store? Or an HTML 5 game portal like Ninja Kiwi?
Plus, the only advantage of an EXE wrapper that I can tell is that you can submit to steam, as 
SullyTheStrange pointed out. I am not aware of any advantages, only the disadvantages of discouraging security warnings to download and play the game, and unnecessarily tieing your game to Windows. Please tell me if there are other advantages I'm not aware of! Because right now it seems the disadvantages outweigh the small advantage (I doubt many people will be publishing to steam in these early days).
Well, not necessarily publishing just to Steam, but how about other game potential areas such as Gamehouse, Big Fish Games, Mac App Store...etc? Or perhaps even publishing and selling your own games? This wouldn't be an issue if CC and C2 were actually interchangeable, them we'd have the best of both worlds already.
There are other dev tools out there that can do this already. The HTML5 version of GameMaker not only creates HTML 5, also an Windows executable version of your game. And the Monkey coding language can spit out HTML5, Flash, Windows, Mac, IOS, Android, and apparently XNA. And of course, there's Gamesalad. But IMHO *none of these* are preferable to C2's ease of use and rapid development.
Anyways, i'm still excited to see where C2 will be in the future :).