Obscure in what sense? I would expect mainpage images to get more clicks than all those exceptions.

Anyway, do you have examples of exceptions were adding either link= or class="metadata" would not be a good idea even irrespective of MediaViewer? Most exceptions I've seen so far would benefit from either being marked as not part of the article content, or marked as "not really an image but something tricky" (CSS magics - a lot of other tools than lightboxes will have trouble with these). Also, for most "tricky" images going to the description page on click is really horrible behavior (see e.g. this issue).