Cawley S, et al. (2004) Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116:499-509, Figure 1

What's wrong with this one?

The three-dimensional rendering of this pie chart is gratuitous, and pie charts are bad anyway, as humans are notoriously poor at comparing areas. The color is gratuitous, too. Any graph that is meaningful only if the numbers are also cited must be viewed as a failure. That the figure is obviously from Microsoft Excel is another embarrassment.

What should have been done?

The authors could have just cited the numbers. Alternatively, a bar plot (without gratuitous 3D) wouldn't be unreasonable.