@Indigo I've heard that the biggest problem was making Samus into an emotional cry-baby with PTSD. The gameplay was extremely linear and used the Wiimote on it's side for a 3D game.
@Indigo That game almost killed Retro, especially after laying off 3/4 of their employees and cancelled 3 other games they were working on. Also, during development the CEO of Retro Studios got caught hosting a porn site which I find absolutely hilarious.
Most of that worry died when the game actually came out and it was still a proper Metroidvania game, just adjusted to an FPS perspective and a 3D map; which I think turned out very well overall. There are certain things that didn't translate too well, they kept a lot of the platforming aspect of Metroid, and they didn't make the jump to first person too well; judging distance with the grapple beam is probobly the worst offender.