Just as a joke, I'd like to see someone do a Skeu UI, the polar opposite, one with such ridiculous degrees of skeuomorphism, that you want to laugh. Maybe have it look like a WW2 era Navy Cockpit.
Comparing VSTs and Ableton are a great example of how too much of either can be a bad thing.
Although Ableton is generally a pleasure to work with, that is due to the way their interface works (especially the time/waveform navigation, I can't understand why nobody has copied that). The flatness of their UI has occasionally confused me (but not as bad as certain skeuoverdosed VSTs).
Cool, I usually kept quiet on these matters because I thought I hadn't really ever given a flat UI a good try. But Ableton definitely counts.
I think the main problem with Flat UIs is the lack of affordance: There is no shared visual language yet to signify the difference between an indicator and an input element. That could be either a switch-button vs a status indicator light (both coloured circles) or a text input box vs a info panel (both rectangles with text).
One way to maybe solve it would be the convention that things brighter than their environment are for input and darker things are for indicators/information. Or vice versa. Because there's no convention yet.