Here goes:
R1:
Mario/Bowser > Earthworm Jim/Slug-for-a-Butt
Ike/Black Knight > Conker/Great Mighty Poo
Kirby/Metaknight > Jill Valentine/Nemesis (thankfully not Tim Taylor/Jill Taylor)
Sonic/Eggman > Katherine/Catherine
Mega Man X > Zero
Bartz/Gilgamesh > Guybrush Threepwood/LeChuck
Ezio/Rodrigo > Donkey Kong/K. Rool
Sub-Zero/Scorpion > Leon Kennedy/Ada Wong
Red/Blue > Jim Raynor/Sarah Kerrigan
Cecil/Golbez > Luigi/Waluigi
Ryu/Ken > Ratchet/Dr. Nefarious
Fox/Wolf > Yuna/Seymour
Samus/Ridley > Kid/Guy
Terra/Kefka > Vyse/Galcian
Chris Redfield/Albert Wesker > Dan/Sagat
Big Boss/The Boss > Tidus/Jecht
Link/Ganondorf > Arthas/Illidan
Amaterasu/Orochi > Tom Nook/Crazy Redd
Zidane/Kuja > Meat Boy/Dr. Fetus
Mega Man/Albert Wily > Banjo/Gruntilda
Phoenix Wright/Miles Edgeworth > Gordon Freeman/Wallace Breen
Alucard/Dracula > Shepard/Saren
Chell/GLaDOS > Ness/Giygas
Frog/Magus > Raiden/Vamp
Cloud/Sephiroth > Lloyd Irving/Kratos Aurion
Kratos/Zeus > Layton/Don Paolo
Pac-Man/Blinky > Crash Bandicoot/Neo Cortex
Solid Snake/Liquid Snake > Crono/Lavos
Squall Leonhart/Seifer Almasy > Laharl/Midboss
Siegfried/Nightmare > Ramza/Delita
Dante/Vergil > Sol Badguy/Ky Kiske
Sora/Riku > BJ Blackowicz/Adolf Hitler
R2:
Mario/Bowser > Ike/Black Knight
Sonic/Eggman > Kirby/Metaknight
Mega Man X/Zero > Bartz/Gilgamesh
Sub-Zero/Scorpion > Ezio/Rodrigo
Red/Blue > Cecil/Golbez
Ryu/Ken > Fox/Wolf
Samus/Ridley > Terra/Kefka
Big Boss/The Boss > Chris Redfield/Albert Wesker
Link/Ganondorf > Amaterasu/Orochi
Mega Man/Albert Wily > Zidane/Kuja
Alucard/Dracula > Phoenix Wright/Miles Edgeworth
Frog/Magus > Chell/GLaDOS
Cloud/Sephiroth > Kratos/Zeus
Solid Snake/Liquid Snake > Pac-Man/Blinky
Squall Leonhart/Seifer Almasy > Siegfried/Nightmare
Sora/Riku > Dante/Vergil
R3 and beyond:
Mario/Bowser > Sonic/Eggman
Mega Man X/Zero > Sub-Zero/Scorpion
Ryu/Ken > Red/Blue
Samus/Ridley > Big Boss/The Boss
Link/Ganondorf > Mega Man/Albert Wily
Frog/Magus > Alucard/Dracula (changed right on the spot!)
Cloud/Sephiroth > Solid Snake/Liquid Snake
Squall Leonhart/Seifer Almasy > Sora/Riku
Mario/Bowser > Mega Man X/Zero
Samus/Ridley > Ryu/Ken
Link/Ganondorf > Frog/Magus
Cloud/Sephiroth > Squall Leonhart/Seifer Almasy
Mario/Bowser > Samus/Ridley
Cloud/Sephiroth > Link/Ganondorf
Cloud/Sephiroth > Mario/Bowser
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