CvS3:
Ibuki vs. B. Jenet
Dudley vs. Rick Strowd
Makoto vs. Kasumi
Alex vs. Tizoc
Gen vs. Lee Pai Long
Retsu vs. Todo
DR Cammy vs. Blue Mary
Sagat vs. Iori (<--- because it's still not official!)
Akuma vs. Mr. Karate
Rose vs. Chizuru
Gouken vs. Tung
Viper vs. Whip
Guy vs. Ryo
Sodom vs. Eiji
Leo vs. Haohmaru
Mai-Ling/Tao vs. Akari
Donovan vs. Asura
Felicia vs. Cham Cham
Anakaris vs. Mudman
Hsien-Ko vs. Mina
Hayato vs. Kaede

Here's my take

Ben 10 vs Capcom

titled; New Generation of Anime Heroes

animation; same as Tatsunoko vs Capcom (intro, attack, super attack, variable combo)

- Ben 10 has their own powerhouse; Kevin Levin. And he'd be a perfect opponent to Capcom's powerhouses; Ken and Ryu

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Square Enix vs Capcom

Beat

He can attack with his skateboard. If you pick Neku as his teammate. Him and Neku will rush at the opponent, doing their own version of the Raging Demon.

Cloud

Wields his Ultima Weapon (final weapon of FFVII). When your super meter fills up, you can perform his signature move; The Omnislash. Takes out 1/2 out of the opponent

His blade beam is one of his normal attacks

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NIS vs Capcom

This would be in the tradition of Cross Edge. Which you'd acquire several NIS and Capcom characters, and the evil lord of doom? M. Bision, his henchmen; Sagat, Balrog and Akuma.

Among the heroes; Ryu, Guy, Warrior [m] - Disgaea, Etna, Zelos - Absolute Blazing Infinity, Zangief etc...

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Fire Emblem vs Street Fighter

A selected few of Fire Emblem fighters use their skills to go up against Street Fighter's best in a MVC/Tatsunoko vs Capcom-esque tournament etc...

Ike

His signature move; Great Aether

Boyd

His signature move; Axe throw, he'd throw several axes at his opponent

Mortal Kombat vs. Street Fighter

Liu Kang vs. Ryu

Kung Lao vs. Ken

Kitana vs. Chun Li

Johnny Cage vs. Guile

Jax vs. Zangief

Sonya vs. Cammy

Raiden vs. Dhalsim

Frost vs. Sakura

Baraka vs. Blanka

Kano vs. Vega

Goro vs. Sagat

Shao Kahn vs. Bison

Shang Tsung/Scorpion vs. Akuma

Not sure who I wanna see Sub-Zero go against but I would want him in the game though.

Alex vs. K'
Abel vs. Ash
C. Viper vs. Elisabeth
Rufus vs. Shen
Cody vs. Silber
Urien vs. Zero
Gill vs. Igniz

Shin Akuma vs. Omega Rugal
The story of this match could be like this. By the end of the 2001 tournament, Akuma was unexpectedly beaten by Rugal. As Akuma lay unconscious, Rugal absorbed Akuma's satsui no hadou and transformed into Ultimate Rugal. Kyo, Terry, and Ryo tried their best to fight Rugal but was beaten. As the match continues, Ultimate Rugal begins to weaken and Iori suddenly woke up in his Orochi form and assaulted him. The match ended up with both Rugal and Iori being badly injured. Akuma then wakes up and decides to fight in his full power and was able to pull of a shun goku satsu on Rugal. Rugal knew he couldn't contain both these evil energies so he decides to pass it on to Akuma in an attempt to live on. Akuma then went in berserk and Ryu turns into Evil Ryu. Evil Ryu and Orochi Iori then begins to face off against the Orochi Shin Akuma and was losing until Ryu was able to conquer his dark side and finishes Akuma off with the shinku hadouken. And that is when the Capcom vs. SNK 2 Shin Akuma ending pops in... With the start of the 2010 tournament(Capcom vs. SNK 3), Rugal and Akuma returns...

Fei vs Law