[eluser]Phil Sturgeon[/eluser]
I agree. They aren't supported well at all. In 1.7.2 they can be hacked but you never could leave $config['uri_protocol'] = 'AUTO' on to support them globally thorough your application as ?foo1=bar1&foo2=bar2 would then become /foo1/foo2.
This is still in 2.0 along with the extra screwyness that is example.com/?/controller when you use anchor() or site_url().
While I understand this is built to support servers without mod_rewrite, CGI PHP, etc there needs to be a middle-ground. Right now I can't think what that is, but its safe to say query string support is not nice atm, even if we can hack it.
