It's not about making the first 3D Zelda, it's about doing something new with the formula or at least delivering something that isn't filled with hand holding and fetch quests.
The design of Metroid Prime was incredibly elegant and well thought out. You didn't need constant reminders from NPCs on how to do the simplest actions. It played out intuitively and delivered stellar atmosphere, scenario design, and gameplay across the board.
At there core, the modern Zelda games are very well done, but there are too many little things that ultimately sour me on each one. You may not agree, and that's fine, but I'm ready for a fresh perspective and I think Retro has handled Nintendo's franchises better than EAD has throughout the last ten years. Metroid Prime is one of the finest games Nintendo has ever published and Retro is responsible for it.