The problem I tend to see is that the refactoring never happens. Instead the system becomes the legacy mess nobody wants to work on and eventually it gets replaced. If you get lucky, it'll be replaced by the people who wrote the first version, but it's more likely to be replaced by a team who weren't there when the first one was built, who will build it in this-year's-shiny, without learning the fundamental lessons of why the first version ended up that way so doom the next version to a similar fate.