[eluser]Randy Casburn[/eluser]
I use AJAX extensively. I'm not sure what I would do without the functionality CI offers as the 'server' component in the 'client/server' pair. Without loading up CI, I don't get all the functionality it offers. So I take advantage of all that but for optimization, I dump everything via 'echo'd json_encode()'d strings as soon as possible and avoid further processing by CI. Certainly avoid the Output class as it provides no benefit unless you are returning HTML to your AJAX requests.
That said, if you wanted to 'create a special php file' because you don't need the framework's overhead...do you really need the framework at all?
Hope this is helpful,
Randy