I don't think for a minute that Prey was in jeopardy of being a bad game, but I do think that perhaps it wasn't turning out as expected. Most companies would be forced to continue with a project that has gone slightly awry, simply because the economics of fronting a new game design once you are well into a project are far too formidable for most. The majority of companies are strapped for resources and locked into a ship date with a publisher. 3D Realms doesn't fall into this category. In many ways I think the news that Prey has had a changing of the guard is good, or at least in the respect that we know 3D Realms isn't going to settle for second-best.
Games are no different.
Sometimes parties with the most genuine intentions for a game just don't move in the same direction. However, there is cause for concern about why the game would get to this point, especially considering the fact that Schuytema had been on the project for over a year. Usually creative differences are evident very early on, and that's why the announcement that he had left came as somewhat of a shock to the industry. One has to wonder what was the straw the broke the camel's back so to speak. All valid questions that are virtually unanswerable based on that current information.