Look, I’m not trying to be an @$$ here. I prefer the Google Authentication app, personally, but I despise the authentication occurring on the same screen as the username/password. It simply isn’t the most effective way to use the 2-Step Authentication model.
The Authy Two Factor Authentication plugin has obviously found a way, which isn’t as disruptive as you want to think. It also seems to me, when their authentication is occurring outside of the WordPress login (username/password) area, it stands to reason other plugins, which perform credential verification tasks, from the same area, would have less problems, not more.
It just seems to me your plugin could play a bigger role, in self-hosted WordPress websites, by aiding in the User Experience, not taking away from it. Tool-tip or not, people are confused by your plugin’s workflow, especially those not using 2-Step Authentication. And, while I’m completely aware, we are way outside of the issue, I first reported and deep into a feature request, it seems to me, making your plugin more useful, less confusing and providing a better over all user experience, would be pretty high on the to do list.