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I did a quick Photoshop of two screen grabs of the sneak peek and lightened the background. The lessening of contrast reduced the blockiness, perhaps at the expense of differentiation, but the desktop program is legible without the dark background.

I compared your interface with Things and the problem that you have is that you need to show nested folders, which they don't have to, so your arrangement has to be more intricate. But many of the comparisons between you are focussed on their more Mac-like appearance. My preference too is for clean, simple lines. Instapaper uses a slight graduation to draw the eye in rather than harsh lines and colour.

I am wondering if you need to keep the traditional stepped arrangement of the full version, but will think through alternatives before posting suggestions.