The Popup is different than the infoWindow in its implementation.
The Popup class is an implementation of InfoWindow that inherits from InfoWindowBase to provide additional capabilities.
Popups provide the following additional capabilities:
•Provides a user interface to navigate through multiple selections.
•Zoom and highlight selected feature.
•Maximize the info window.
The popup has events and methods that the infoWindow doesn't have, such as the "selection-change" and "getSelectedFeature". For example, in this sample, this code insertion returns the selected feature.
var graphic = popup.getSelectedFeature();
//end of code
var parcelsURL = "http://sampleserver3.arcgisonline.com/ArcGIS/rest/services/BloomfieldHillsMichigan/Parcels/MapServer";
If you want to get the selected feature, why not listen to the map's click event or, if you're using a FeatureLayer, utilize its "selection-complete" event, which returns an array of graphics.