As the conclusion to a trilogy would suggest, the Metroid Prime series seems to be over, and Retro Studios confirmed to Yahoo! Games they're moving onto something new:
"We are taking a break from Metroid series and from Samus," said Metroid Prime 3 Game Director Mark Pacini. "I'm sure there will be other [Metroid] titles created, [but] as far as the Retro Studios is concerned, we're taking a break for a little bit."