I haven't played Skyrim yet, and Zelda is an awesome game (what I've played of it so far) but you'd have to be a tremendous fanboy to say that Zelda should have won 100%. What is it about Skyrim that makes it so inferior in your opinion? I didn't have much hope for Zelda winning, but any I did was gone as soon as Batman beat it for best Action/Adventure title.
The VGAs are a 2 hour advertisement spot. Nothing less, nothing more. There were only 6 awards handed out on air as opposed to 13 trailers (ads) with even more unrelated ads for commercial breaks.
I'd say the actual awards were the best part of the show. They were either deserved or at least justifiable.
As for the people who did the voting and nominations, there are a lot of names I highly respect on the list:
Andy McNamara (Editor in Chief, Game Informer Magazine)
Brian Crecente (Editor in Chief, Kotaku)
Chris Baker (Senior Editor, Wired Magazine)
Chris Kohler (Games Editor, Wired.com)
Chris Slate (Editor-In-Chief, Nintendo Power Magazine)
Christopher Grant (Editor in Chief, Joystiq)
Dale North (Editor in Chief, Destructoid)
Francesca Reyes (Editor in Chief, Official Xbox Magazine)
Gary Steinman (Editor in Chief, GamesRadar)
Geoff Keighley (Host, SPIKE)
Jeff Gerstmann (Editor in Chief, Giant Bomb)
Jeff Jensen (Senior Writer, Entertainment Weekly)
Jerry Holkins (Writer / Co-Creator, Penny Arcade)
John Davison (VP of Programming, GameSpot & Metacritic)
Logan Decker (Editor in Chief, PC Gamer Magazine)
Lou Kesten (Reviewer/Editor, The Associated Press)
Mike Krahulik (Artist / Co-Creator, Penny Arcade)
Mike Snider (Technology Reporter, USA Today)
Rich Greenhill (Director of Content and Programming, Yahoo Games)
Sam Kennedy (Director of Audience Generation, IGN.com/1UP.com)
Scott Alexander (Freelance Writer, Playboy & Family Circle)
Shane Satterfield (VP of Content, SPIKE Digital Entertainment)
Stephen Totilo (Deputy Editor, Kotaku)
Tal Blevins (VP Games Content, IGN Entertainment)
Tina Amini (Assistant Editor / Video Games Channel Manager, Complex Magazine)
Edit: Also, why wouldn't they take the chance to induct The Legend of Zelda into the Hall of Fame on its 25th Anniversary and a year a flagship entry in the series (not something terrible like Spirit Tracks or Phantom Hourglass) is released? Seriously. The VGAs are terrible, but for none of the reasons you've listed. It's also a lot better than it was in previous years.