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I think of "retro" as pixel-based and early 3D games that were sorta killed during the PS1/Saturn/N64 era.
Once we get into more advanced 3D / Polygonal games (PS2/GameCube/Xbox), it's a different era; but it's not due to the visual shift alone, but the design philosophy and craft/code itself. I would consider them "modern" and point to series like Zelda as an example.
Games like WindWaker feel more connected to Breath of the Wild than it does to Link to the Past or even Ocarina of Time. And I think the same goes for series like Mario, Metal Gear, and so on.