I have a responsive WP blog that I converted into an application with cordova. (and added some extra features).
My idea would be to prompt an user that uses mobile to install the application if he run the site in his mobile browser instead in his application.
Something like:
if (isMobile() && !isApplication()) {
var download = prompt('Would you like to install the application instead ?');
....
}
Maybe such a plugin does already exist in WP ?