Metroid Prime 3 was released in 2007, but VideoGamesChronicle has discovered that a lot of the game’s core team is still at Retro Studios. They said that “a core team of around 50 people worked full-time on the 2007 Wii shooter and around 27 remain at the Texas-based developer”. In fact, 5 of the 11 designers that worked on Metroid Prime 3 are still at Retro, as well as “4 contractors that were made permanent”. As for the original Metroid Prime, which released in 2002, it is a different story. VideoGamesChronicle says that “less than ten of the 40-plus team members remain at Retro and virtually all of the lead creators have moved on”.
Thanks to Christian Paredes for the tip.