Reminds me of the work of a certain wiki I've created a number of matches, not just anime on:
Deadliest Fiction Wiki, create your own Deadliest Warrior-style match
Some anime-related matches I created:
Bandou (Elfen Lied) vs Revy (Black Lagoon)
Winner:Bandou
Also, speaking of Saito, here he... almost simply walks into Mordor
Shuya Nanahara (Battle Royale) vs Gai Tsutsugami (pre-Episode 12 version) (Guilty Crown) Winner: Gai
Saito Hiraga (Zero No Tsukaima) vs Shu Ouma (Guilty Crown) Winner: Saito
Kohta Hirano and Saeko Busujima (Highschool of the Dead) vs Yukiteru Amano and Yuno Gasai (Mirai Nikki) Winner: Kohta and Saeko
Akemi Homura (Madoka) vs Nanoha Takamachi (Nanoha) OK, this one is going to be contraversial with some people, namely because HomuHomu wins this one even when I nerfed her for fairness sake. To be fair, magic shields are, according to StrikerS (I think Fate says something to this effect) are not optimized to deal with mass-based weapons, and Homura has plenty of those! As for full powered Homu, she would absolutely curb stomp Nanoha with her time manipulation IMO.
Either way, in my ending to the match, both survive, and it is awesome, even if it flys in the face of Urobuchi's notes.
Spoiler for Nanoha vs Homura battle ending: Why Are We Fighting?! Lets Go Kill Kyubey!:
(insert battle scene- available at link above- here)
"Why?", Nanoha asked, "Why are you doing this?"
"What?", Homura asked, "You can talk, you're not a witch, are you?"
"What are you talking about?", Nanoha asked.
Homura explained that she was a magical girl, a girl who was given magical powers and one wish by a being known as Kyuubee, in exchanged for being forced to fight monsters known as "witches"... and for allowing Kyuubee to harvest the energy from their inevitable demise. She stated that she tried to kill Kyuubee twice, but each time another Kyuubee with the same memories and personality of the original came, and told her "he has many bodies".
"I am Nanoha Takamachi, Time Space Administration Bureau", Nanoha said, "I think know what this Kyuubee is doing to create his extra bodies."
Two weeks later, a cloning facility on an alien planet.
Nanoha fired off countless blasts of energy at hundreds of "Kyuubees" that came at them. The creatures were only about the size of a house cat, but, as it turned out, they could fire powerful beam attacks. Homura helped Nanoha cut them down with an M249 SAW she had taken out of her "hammerspace".
Finally, they made it to the center of the cloning facility. Homura got out an AT4 and fired off a rocket at the device making all the clones, blowing them apart, and took out the teleporter they used to get to Earth, for good measure.
Nanoha then grabbed Homura and blew a hole through the roof and flew upward as the factory exploded below them.
Author's Analysis
As there was a tie on the on-site votes, but a second Homura vote on another site I advertised this battle on, I created this ending where both survive, but Homura actually manages to overpower and "befriend" Nanoha.
I have a whole bunch of other matches featuring anime characters, and others with real people, video games/movie/novel/etc characters, and a number where characters from two different media fight each other.