Dark Link (working for Ganon)
Agahnim (but really Ganon)
The Nightmare in its various forms (among them a dead ringer for Ganon)
Ganondorf (turns into Ganon)
Onox and Veran (and then Ganon)
Vaati (and then Ganon)
Zant (and then Ganon)
How many of those guys appeared in Mario's big block buster titles as main villains? Let's see...
Super Mario Bros-Bowser
Super Mario Bros 2-not sure never cared to play it.
Super Mario Bros 3-Bowser
Super Mario World-Bowser
Super Mario 64-Bowser
Super Mario Sunshine-Bowser
New Super Mario Bros-Bowser
Super Mario Galaxy-Bowser
New Super Mario Bros Wii-Bowser
Super Mario Galaxy 2-Bowser
Super Mario 3DS-hmm, I wonder if King Boo is returning as the main villain of the series. Oh wait Bowser is and is very very very likely to be in this one.
Let's put it this way. When ever someone thinks of Super Mario they know that Bowser is his main arch nemesis. Same thing with the Legend of Zelda. We are finally getting a Wii Zelda title for the first time that is said to be a really big game and Nintendo is going to say "screw Ganon"? He's only been absent 5 years now. People claim that He can't be in it because his "Origin" was in Ocarina of Time. Who says Ganondorf is the same guy? They're always different Links, why not different Ganons? Pig form any form. This game can't be perfect in my eyes if I know Ganon is going to be gone another 3-6 years. Who knows when the Next Zelda will come anyway? Just like Bowser. They can't just announce a huge important Mario game and try to create a new villain to replace Bowser. Bowser is already established and very popular just as Ganon/dorf is. If this game is truly the first in the series "timeline wise" then why not make Ganondorf the villain we all know and love be the start of evil so that way we know how far back the Link vs Ganon/dorf thing goes.
Link vs Ganon forever!
EDIT: It's not that I don't want to see a new villain but when Ganon's been gone this long I just want to see him return. I could understand if they were releasing them every 2 years but we just know that's not happening unless they give us new handheld titles a year or two after the big console title has been released. But we could get big quality Zelda games without our Ganon with the 3DS now. So only time will tell.