The biggest disadvantage, in my opinion, that browser based games have when compared to exe's is that they are bound to the browser, and the browsers functionality comes first. This means making a game that uses the mouse, arrow keys, space, or any other key the browser uses, will be awkward.
If you use the arrow keys then you can scroll the page unintentionally (which happens for me since c2 apparently exports a really large page for some reason. I've resorted to using the numpad for now), same thing with space. With the mouse if you click and hold you're essentially selecting stuff on the page, and if you then drag too far the screen will scroll.
Now, when I preview a project, the game is centered on the page with a border and black background and I don't get these problems, but when I've exported the thing and run it from the net I get the white backdrop and the problems I listed are present. I'm not sure why the preview and exported pages are different. Especially when the preview page is 'better'. The keyboard issues don't seem to be present on the arcade though, but if I click and drag the screen scrolls.
I dl'ed the Bastion trial from the Chrome store. Pretty nifty. but I'd rather get it from Steam, because the Chrome App runs at a set resolution and there's no settings at all apart from controls and subtitles.