It wasn't the beach itself that bothered me, it was that the whole game took place on it. Those visuals get a little repetitive. Mario 64 had all sorts of different areas - snow, lava, caves, mountains, grassy fields, a haunted house and more. Going from everything that Mario 64 brought to the table, to Mario Sunshine, it was kind of a let down.
On the subject of Sonic Adventure, yeah the first level starts you off on a beach, but that was to be expected. All Sonic games start off with some beautiful level like that. Also, while I do agree that too much of the game was done for you (the loops and everything), it was still fun. I wish they'd make a real Sonic game where all the levels are like that (but not in the stupid way they did it with Shadow the Hedgehog).
Lastly, Wind Waker wasn't going for pretty visuals. Most people disliked the graphics of the game. While I do think that the game did have incredible graphics at some points (that first dungeon, with all the fire and lava is amazing), they're actually pretty bland. I don't think the graphics were bad, I thought they worked well with the sailing aspect, but I think the game would've been more enthralling with realistic graphics.