[eluser]BrianDHall[/eluser]
To get the functionality you want you need to remove autoloading entirely, and instead load your desired libraries (and such) via $this->load functionalty. This should be handled in a controller either in a function or in a constructor.
So for instance your Main controller constructor loads all your helpers and goodies and such, and then you have an Thin controller that loads nothing at all. Your autoload would then contain only things you need absolutely everwhere,.
There is no way to bypass autoloads defined in autoload.php per controller, because autoloading is performed too early to interupt.
Important caveat: You might find that the performance difference is so minor that you just don't care, but depending on application scale and just what all you autoload you might need to take this slightly more careful approach of loading a library only when you are pretty well sure to need it, or only when something is very very light.