Handwritten digits actually is a pretty good domain for deep nets, and the poor performance achieved in the article's case is due to the implementation (it needs deeper net, convolutional layer, etc). In that case much better (99%+) results have been achieved by deep nets for digit recognition. In fact, Hinton (in his Coursera course) recommends this domain for studying deep nets, since it is so well understood.

(Ben I know you're aware of all this already, but I just wanted to clarify for those who aren't as on top of the research as you)