> On desktops, it's not clear until you hover that it's even an interactive element.
Have you considered that this is due to you and others being conditioned to believe that beveled/3d elements indicate interactivity whereas flat elements do not? Maybe a change is in order...
Also related to the abandonment of "fake" depth in web design is the latest A-List-Apart article, "Material Honesty" - http://alistapart.com/article/material-honesty-on-the-web