I've often thought about evolutionary engineering like this, comparing it to biological systems. The human body (and really all biological life) is a remarkable machine -- it runs for decades, much longer than just about anything people build, and under most circumstances can repair itself quite impressively. But if it needs repair beyond what it can do itself, you run into a harrowing mess, with difficulty swapping in new parts, some parts doing double duty, difficulty separating various systems, etc.

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?