I know there is a similar topic at http://wordpress.org/support/topic/feature-request-ask-for-code-on-second-page but I felt this was enough of a difference to post a separate request.
The biggest issue I have with this plugin, is in how it negates the stored usernames/passwords from working. I allow Safari to save my Username/Password, for each of my WordPress websites. When the new OS X Mavericks comes out, these passwords will be part of those sync'ed over iCloud, for use on all my other devices. I do not want Safari to stop auto-populating the Username/Password, but I still want to be asked for the Google Authenticator Code.
In addition, this plugin renders the WordPress iOS app, completely useless. When this plugin is installed, WordPress iOS cannot connect to the website. I know it is it's own app, but I'm assuming the issue could be resolved by separating the Username/Password screen from the Google Authenticator screen. Ultimately, I want to use the Google Authenticator on the iOS app, as well.