Despite developing the first Metroid Prime game on the GameCube, Retro Studios will not be developing Metroid Prime 4 according to reports.
Nintendo didn't reveal who will be taking over the Metroid Prime franchise, but Nintendo of America senior product marketing manager Bill Trinen revealed that Nintendo Kensuke Tanabe will help lead the project alongside "a talented new development team." It's unclear if this development team is part of an internal group in Nintendo, or otherwise.
Tanabe has served as a producer on every Metroid Prime game developed by Retro Studios, as well as Metroid Prime Federation Force. So Tanabe is definitely familiar with the Metroid Prime franchise. Retro Studios' most recent Nintendo title was Donkey Kong Country Tropical Freeze, before revealing the company is working on an unannounced title for Nintendo.
We will have more details as the story develops.