I tried looking through the extensions menu, but could not see it listed so I was a bit confused on how it was doing this.
So, I uninstalled the software and then the next time I did a download, I got to a page that said "Missing plugin".
Having another look in the menu, I cannot see anywhere to configure plugins, only extensions - The extension page is "Chrome://extensions", so I took a stab in the dark and typed "Chrome://plugins" and it worked!
On this page, I was able to fully remove the plugin I no longer wanted, but I got a surprise and found "Chrome PDF Viewer"
I disabled Adobe PDF reader and enabled this.
On it's first run, it is a little slower (I guess the plugin was starting), but once it was loaded, everything about it is much faster and it enables me to highlight and copy text in PDFs where Adobe's reader sometimes fail.
I have no idea why this is disabled by default, but I am certainly going to be using this from now on. Lets just hope Google come out with a Flash alternative soon!