Zelda and Mario for a short while were the franchises to be the "first" in a lot of things for the mainstream home consoles. So they really set standards for prototypical adventure and platformer genres for both 2d AND 3d. So yes they have earned their iconic status.
But I'm not sure where your criticism comes from overall. Fans hated windwaker for being too different (I loved it, but it has low replay value with the easiest gameplay I've ever encountered). And fans hated Twilight for being too similar. And around that time is when shooters and music games were all the rage anyways. No one cared about zelda these past two generations. It hasn't been critically acclaimed in recent years.
Mario Sunshine was universally hated as well by both non-mario gamers being able to use it as an example fo why nintendo is just for kids, and by mario-gamers who hated the water backpack. Galaxy was TRULY inventive for the Mario series if if Galaxy 2 wasn't anywhere near as good as Galaxy 1.
On Zelda you are wrong because it is not reverred anymore. Mario you may be right on... but nsmbw did not get amazing scores despite it being an amazing seller
