As I understand things, Duke's problem is more that 3D Realms is run by programmers, not businessmen.
George Broussard owns the company, and he's head of the Duke Forever team. So he can do whatever the hell he wants as long as the company doesn't go bankrupt. And what he wants is to integrate every feature under the sun(I'm sure he calls it making Duke Nukem Forever the best game possible, or something similar).
Basically, Duke has a REALLY bad case of feature creep, and won't make it out until Broussard freezes the feature set.