Sometimes companies just change staff slowly, and eventually stop being the same company. They start making different games from what they made before, because different people work there now. Look at how much Sega's Sonic Team changed over the years. Look at the wild differences between 90's Final Fantasy and post 2000 Final Fantasy. Could Retro Studios even make another Metroid Prime game? I doubt it. At least not a good one.
The good thing about this though is that if this is true, the creators of amazing games like DQ8, Rogue Galaxy, and Dark Cloud will just move their talents to other companies. It happens a lot in comic books. One writer leaves Marvel or DC to join the opposite side. Or they start writing for Image or an indie book. Suddenly those creators have freedom again that they lost in their years working for their old bosses. And their writing/art becomes so much better for it.