The app-specific passwords are a feature and if you prefer the extra security over being able to use apps that don't support 2-factor, then you can choose not to use them, and get the full security benefits of 2-factor. It's just that, short of expecting every single third-party client app to implement 2-factor authentication or not allowing access to any that don't, there's no alternative to the app-specific passwords.

They are strictly better than using a single password for everything though, in that they are unique and strong (due to being automatically generated and 16 characters long), and easily revocable.