Since there is no native way to do this ,Here is the less intrusive solution i found (dont add any 'old' prototype methods):
var ListenerTracker=new function(){
    var targets=[];
    // listener tracking datas
    var _elements_  =[];
    var _listeners_ =[];
    this.init=function(){
        this.listen(Element,window);
    };
    this.listen=function(){
        for(var i=0;i<arguments.length;i++){
            if(targets.indexOf(arguments[i])===-1){
                targets.push(arguments[i]);//avoid duplicate call
                intercep_events_listeners(arguments[i]);
            }
        }
    };
    // register individual element an returns its corresponding listeners
    var register_element=function(element){
        if(_elements_.indexOf(element)==-1){
            // NB : split by useCapture to make listener easier to find when removing
            var elt_listeners=[{/*useCapture=false*/},{/*useCapture=true*/}];
            _elements_.push(element);
            _listeners_.push(elt_listeners);
        }
        return _listeners_[_elements_.indexOf(element)];
    };
    var intercep_events_listeners = function(target){
        var _target=target;
        if(target.prototype)_target=target.prototype;
        if(_target.getEventListeners)return;
        if(typeof(_target.addEventListener)!=='function'||typeof(_target.removeEventListener)!=='function'){
            console.log('target=',target);
            throw('\nListenerTracker Error:\nUnwrappable target.');
        }
        // backup overrided methods
        var _super_={
            "addEventListener"      : _target.addEventListener,
            "removeEventListener"   : _target.removeEventListener
        };
        _target["addEventListener"]=function(type, listener, useCapture){
            var listeners=register_element(this);
            // add event before to avoid registering if an error is thrown
            _super_["addEventListener"].apply(this,arguments);
            // adapt to 'elt_listeners' index
            var uc=(typeof(useCapture)==='object'?useCapture.useCapture:useCapture)?1:0;
            if(!listeners[uc][type])listeners[uc][type]=[];
            listeners[uc][type].push({cb:listener,args:arguments});
        };
        _target["removeEventListener"]=function(type, listener, useCapture){
            var listeners=register_element(this);
            // add event before to avoid registering if an error is thrown
            _super_["removeEventListener"].apply(this,arguments);
            // adapt to 'elt_listeners' index
            useCapture=(typeof(useCapture)==='object'?useCapture.useCapture:useCapture)?1:0;
            if(!listeners[useCapture][type])return;
            var lid = listeners[useCapture][type].findIndex(obj=>obj.cb===listener);
            if(lid>-1)listeners[useCapture][type].splice(lid,1);
        };
        _target["getEventListeners"]=function(type){
            var listeners=register_element(this);
            // convert to listener datas list
            var result=[];
            for(var useCapture=0,list;list=listeners[useCapture];useCapture++){
                if(typeof(type)=="string"){// filtered by type
                    if(list[type]){
                        for(var id in list[type]){
                            result.push({
                                "type":type,
                                "listener":list[type][id].cb,
                                "args":list[type][id].args,
                                "useCapture":!!useCapture
                            });
                        }
                    }
                }else{// all
                    for(var _type in list){
                        for(var id in list[_type]){
                            result.push({
                                "type":_type,
                                "listener":list[_type][id].cb,
                                "args":list[_type][id].args,
                                "useCapture":!!useCapture
                            });
                        }
                    }
                }
            }
            return result;
        };
    };
}();
ListenerTracker.init();
EDIT
Suggestion from @mplungjan: modified to listen to wrappable targets (singleton|constructor). 'init' tracks Element and window .
exemple with other wrappable target:
ListenerTracker.listen(XMLHttpRequest);
Suggestion from @kodfire : You may get optionals arguments with the args property.