First off, you say we feel this way but are actually in denial, but not to take offense? Uhm, please don't purport that you know what everyone else is thinking. As a matter of fact, reviews of the game are overwhelmingly positive, from gamers and the gaming media alike.
Secondly, Link has never been disproportioned?http://tuxnes.sourceforge.net/snaps/zelda-snap-0002.gif
This took me two minutes on Google to find. Now, I know that you're going to say "That was because of hardware limits!" Then why did they make a proportioned Link for Zelda II?http://nesnexus.freewebsites.com/screens/zelda2-5.gif
Well, you could say Link evolved. However, they switched him back to his Super-Deformed, cartoon-y self with A Link To The Past. It would have been easy to follow Zelda II's style, wouldn't it? Hmm, Link's more
realistic foray was a bad design choice? Odd. That's certainly not the consensus I get with Ocarina of Time.http://www.gamefans.de/zelda3/z3abb4.jpg
And then we have Ocarina Of Time.http://www.zeldaguide.com/6.jpg
I think it's fair to say OoT's Link is more realistic, right? Well, alright then, now we're getting somewhere. However, I fail to see how A Link To The Past's disproportionate Link had any effect on the gameplay. Sure, Link may be dancing with fairies in a tunic and wearing a pink border around his hat, but ALLTP is considered one of the greatest Zelda games ever.http://gallery.consumerreview.com/vgr/gallery/pictures/celda.jpg
Now, we have the new Link. A little kid with gigantic eyes and short arms. Hey, guess what? The gigantic eyes serve a purpose. You know what's also odd? This Link is the greatest swordfighter in Zelda history. He pulls off things Ocarina's Link couldn't dream of. Zelda II's Link would Super Jump away in fear. You, however, are judging the game by character design.
Isn't that the equivelant of me looking at a little person and saying, "Hah, what was God THINKING?"
Edit: Just for the record: CEL-SHADING. He is not being created by use of Biology.