- Too linear
- Superfluous combat that was just an extension of puzzles
- Too large a focus on items being used as keys to progress through the game
- Not enough landmarks and open-ended areas that exist for the sake of being explored
- Not enough focus on RPG mechanics (doling out of equipment has been very controlled by the story in recent Zeldas)
- Not enough weapon variety
Sounds like a list of what Zelda does well with room for improvement to me

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My dream game would be a new 3D Metroid that follows the gameflow of Metroid Prime and Super Metroid, but manages to tell a more interesting science fiction/science horror story with minor religious/spiritual overtones playing off the energy sucking ability of Metroids, the power suit of Samus Aran, and Chozo science, spiritualism, and history. A story that bridges, say, Alien and science fiction anime, which has always been the telos of Metroid in my mind rather than the Sunday morning cartoon approach of Tanabe and the melodramatic approach of Sakamoto of late. I'd also like a more characterized Samus that actually respects the older games and I can enjoy. Samus is tasked with finding, say, a famed, eccentric archaeologist (who may or may not be dead) and this takes her to a forgotten or hidden planet that reveals deep secrets about the Chozo. She gets stuck there for some time and the quest says a lot about her, Metroids, Chozo, etc.
Now story can very obviously mess up the gameflow so it would have to be mostly through lore, boss events, etc. and not dictate how you progress through the labyrinth. Gameplay does this through gadget upgrades.
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Second dream game would be FE meets Matsuno style story. Give me an epic, nerdy war story SRPG with character driven armies and gameplay evolved from FE...
Third dream game would be an epic strategy game about the Peloponnesian War that really captures the feel of Thucydides in its presentation and somehow manages to present Greek polis style war and politics in an approachable way.
Also, always the inchoate wish for the greatest JRPG of all time.