Let's Vote!
FOXHOUND Division
1.Solid Snake (Metal Gear Solid series)
2.Vivi (Final Fantasy IX)
3.Terra Branford (Final Fantasy VI)
4.Geno (Super Mario RPG)
5.Hero (Dragon Quest VIII)
6.Phoenix Wright (Ace Attorney series)
7.Sonic the Hedgehog (Sonic series)
8.Nathan Drake (Uncharted series)

I envisage a showdown between Snake and Drake at the peak of this bracket.

Triforce Division
1.Link (Legend of Zelda series)
2.Red Mage (Final Fantasy I)
3.Crash Bandicoot (Crash series)
4.Zidane Tribal (Final Fantasy IX)
5.Darth Revan (Knights of the Old Republic)
6.Lloyd Irving (Tales of Symphonia)
7.Gordon Freeman (Half-Life series)
8.Chell (Portal series)

Probably a Link win here but I am really rooting for Lloyd Irving, I love the guy.

Egg Division
1.Ma Chao (Dynasty Warrior series)
2.Locke Cole (Final Fantasy VI)
3.Jill Valentine (Resident Evil series)
4.Junpei Iori (Persona 3)
5.
6.Sazh Katzroy (Final Fantasy XIII)
7.Augustus Cole (Gears of War series)
8.Naoto Shirogane (Persona 4)

A strong Persona and Final Fantasy bracket here, but I can easily see the Cole Train steamrolling to victory.

Metroid Division
1.Samus Aran (Metroid series)
2.Mega Man (Mega Man series)
3.Donkey Kong (Donkey Kong Country series)
4.Ike (Fire Emblem: Path of Radiance)
5.Balthier (Final Fantasy XII)
6.Black Mage (Final Fantasy I)
7.Master Chief (Halo series)
8.Commander Shephard (Mass Effect)

Feel kind of bad for dropping Yoshimistu, but Commander Shepard most likely has this. Still rooting for Balthier though!

Umbrella Division
1.Leon Kennedy (Resident Evil series)
2.Alicia (Valkyria Chronicles)
3.
4.Largo (Valkyria Chronicles)
5.Guile (Street Fighter series)
6.Zell Dincht (Final Fantasy VIII)
7.
8.Dante (Devil May Cry series)

Quite a few match ups where I knew neither combatant. That's a bit disappointing on my part. Perhaps a Dante victory here?

Henshin Division
1.Viewtiful Joe (Viewtiful Joe series)
2.Yuri Hyuga (Shadow Hearts)
3.Rydia (Final Fantasy IV)
4.Altair (Assassin's Creed)
5.
6.Ecco the Dolphin (Ecco the Dolphin)
7.Fox McCloud (Star Fox series)
8.

Altair vs the Prince? Oh man xD

Heck Division
1.Clank (Ratchet and Clank series)
2.Sackboy (LittleBigPlanet)
3.Banjo (Banjo-Kazooie series)
4.Ezio (Assassin's Creed)
5.Sephiroth (Final Fantasy VII)
6.
7.Tira (Soul Calibur series)
8.Mitsuru Kirijo (Persona 3)

It's never Lupus, right? Also surprised to see Sephiroth in a "hero" contest but I suppose it still works.

Vector Division
1.KOS-MOS (Xenosaga series)
2.Guy Cecil (Tales of the Abyss)
3.Big Boss (Metal Gear Solid series)
4.
5.Courier (Fallout: New Vegas)
6.Georg Prime (Suikoden series)
7.The Lone Wanderer (Fallout 3)
8.Sora (Kingdom Hearts series)

My Lone Wanderer and Courier would probably win this contest hands down, but man they've gotta face Georg Prime. LOOK AT HIS NAME EVEN.