Re-writing rough JS code with loads of jQuery plugins
On the whole, I think you need to work on keeping it simple.


I would not write my own cross-browser event handling function if I use jQuery, I would leverage what jQuery provides.
This:

/* standard JS */
function InitStandard(jQuery) {
    //get device information
    this.device = new Device();

    // initialise jQuery, if device is capable
    if (this.device.quality === 1) {
        this.jqueryPlugins = new InitJquery(jQuery);
    }
}

/* initialise standard JS on load and pass in the jQuery object */
(function init(jQuery) {
    var js = new InitStandard(jQuery);
}(jQuery));


could be 

(function InitStandard(jQuery) {
    //get device information
    this.device = new Device();

    // initialise jQuery, if device is capable
    if (this.device.quality === 1) {
        this.jqueryPlugins = new InitJquery(jQuery);
    }
}(jQuery));


Because you are not using var js anywhere.
Also, 1 should be assigned to a properly named constant like ADVANCED_DEVICE
addEvent(window, 'load', init); could be $( init )