Visually references are visible on the bottom of the page. It's there on the bottom where you can spot problems. It should be there were you can fix them.
When I want to refactor references (e.g. to convert plain links to templates) I often find myself looking through large parts of text for a minute or two. So just looking for a standard reference is hard... And refrences can also be inside an infobox which makes them even harder to spot.
So it would be great if either VE would simply show a list of links in the references list popup. Or maybe make arrow-links in the list work (I mean those links on the left side of the list).