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In a Q&A, the developers revealed that Shuma-Gorath was one of the first Marvel characters proposed, but Marvel was reluctant to allow them to use him, but Capcom eventually convinced them that he is popular and a big part of the series history, eventually leading to his inclusion as DLC.
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When Deadpool starts his Level 3 Hyper Combo, he strikes a pose and says "Boop-oop-a-doop". This is a reference to the catchphrase of the classic cartoon character, Betty Boop.
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Sentinel's character bio specifies his serial number as COTA-94. This is a reference to Children of the Atom; the first Capcom fighting game to feature X-Men characters, released in 1994.
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When Deadpool defeats Magneto he says "I just beat Mag-freakin'-neto! Where your curly mustache at?!" This line comes from a video featuring the gameplay and voice of Marvel Vs. Capcom 2 world champion Michael "Yipes" Mendoza, in which he says the same thing.
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There is a mistake in Chris Redfield's ending. In the ending, Chris has Albert Wesker on trial with Matthew Murdock (Daredevil) prosecuting. Matthew Murdock was never a prosecutor, as he is a defense attorney.
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There is code in the game's data that would suggest that Doctor Octopus would have appeared in the game as a playable character.
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Director Ryota Niitsuma has stated that Blade was considered as a playable character for the game, but they decided not to include him as they didn't want too many characters that use swords.
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