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Guile has a special introduction against Rugal Bernstein, where he cuts a statue of himself in half with a Sonic Boom before Rugal destroys the base with a Reppuuken. This is in reference to The King of Fighters '94, where Rugal has a statue of Guile amongst his various trophies. Given how he makes his "statues", this implies Rugal had fought Guile in their universe and used his body to create his statue.
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In an interview with Polygon, Capcom's Hideaki Itsuno confirmed that a sequel to Capcom vs. SNK 2 started development shortly after work was finished on the game. Capcom vs. SNK 3 was meant to be the last 2D fighting game in the series, but along the way it ended up becoming a 3D fighting game. The project was canceled due to SNK's bankruptcy, and the remaining 3D assets from it were repurposed for another canceled 3D fighting game, Capcom Fighting All-Stars: Code Holder.