I like how you gave up on the number pairing early.

(SPOILER)
FOXHOUND Division
1.Solid Snake (Metal Gear Solid series)
4.Sonic the Hedgehog (Sonic series)

Triforce Division
1.Link (Legend of Zelda series)
2.Cecil Harvey (Final Fantasy IV)

Egg Division
1.Crono (Chrono Trigger)
2.Kirby (Kirby series)

Metroid Division
1.Citan Uzuki (Xenogears)
2.Balthier (Final Fantasy XII)

Umbrella Division
1.Kid (Chrono Cross)
4.Dante (Devil May Cry series)

Henshin Division
2.Rydia (Final Fantasy IV)
4.Fox McCloud (Star Fox series)

Heck Division
1.Earthworm Jim (Earthworm Jim series)
3.Agrias Oaks (Final Fantasy Tactics)

Vector Division
1.KOS-MOS (Xenosaga series)
4.Sora (Kingdom Hearts series)