Please do not take this the wrong way, i am not against having an application for the authenticator/RSA key.
I do think that using an application that you can install on multiple devices to produce your authentication key is a TERRIBLE idea. The only way i would support it personally is if it were a SEPARATE key that required you to have a standard authenticator or gave the option to keep one which you could use to shut down your account or at least shut down the application controlled authenticator.
When you allow the ORIGINAL KEY to be transmitted, it can be intercepted. right now, the only way for someone to get your authenticator compromised is to gain access to the database that SE holds for authentication (in which case we would all be screwed no matter the authentication type), but when there is an mobile phone application, spyware could easily glean your original key.
TL;DR I have an unpopular opinion based on security paranoia.
