The warning is a bit annoying, but without it attacks like this would be harder to spot: http://feross.org/html5-fullscreen-api-attack/ (it's just a proof-of-concept, no malicious payload)
Who are all these people who apparently run their browser maximized? Web pages generally get worse as the window gets wider. (Unless, of course, they control their own width, but that's its own obvious prompt to stop wasting all your screen space.)
No, it would still have to be a small squarish display. Fixing the aspect ratio won't fix the problem that you have way more space than the website will take.