It's also not extensible at all, which is a big problem for software engineering. An evolutionarily derived codebase might do really well at the problem that provided the parameters for its initial evolution, but trying to get it to do something else might be difficult or impossible. I suppose you could use more evolutionary iterations to get it to do something else, but maybe it'd be easier to start from scratch at that point?
One of the papers: http://www.informatics.sussex.ac.uk/users/adrianth/ices96/pa...
They drew a graph of any units on any connected path from input to output, and then ran a search to see if any others had any effects, by clamping random units' values to 0 or 1 and seeing if that degraded the result. They found that one unconnected unit in particular degraded performance significantly (the bottom/right gray-colored one in Fig. 7): it had several active connections routed through it, but its own output went nowhere. So they hypothesized that it was modulating the signal in a way not captured by the mathematical abstraction of the FPGA as a digital circuit.