Art Shift: Reuse of Street Fighter Alpha sprites, and the ensuing clash in art style and animation quality, was one of the strongest complaints. Morrigan's constant reuse of her very first sprite is still a vivid running joke in many circles.
Bowdlerise: The North American version is notable for its level of censorship not found in any other Capcom fighting game. Moves with "Genocide" (Tiger Genocide and Genocide Cutter) in them were replaced with "Destroyer". Yamazaki's S&M move had its name changed as well. Rugal calling out his Genocide Cutter was replaced with a generic grunt, and Sagat cuts off the "Genocide" part from his Tiger Genocide, and again, replacing it with a generic grunt. God Rugal was changed to Ultimate Rugal. Due to Viewers Are Morons, Shin Akuma was untouched and became a Bilingual Bonus.
Comeback Mechanic: The most obvious examples are S-Groove (where an opponent gains infinite meter while close to death and gains access to SDM moves and Level 3 moves should they charge up the meter in this state) and K-Groove (attacks do more damage and they receive access to a Super Move once its full) but only lasts a limited amount of time and ends the moment the Super Move is used.
Composite Character: In the sense of gameplay, most of the CvS1 vets play like a fusion of their Normal and Extra versions, incorporating specials and supers from both move lists.
Dialogue Tree: The games are full of this, with stuff like Geese throwing a Reppuuken at Bison to blow his cape away.
Market Based Subtitle: Millionaire Fighting became Mark of the Millennium when it was ported overseas, though the announcer still says "Millionaire Fighting 2001!" at certain points on the character select screen.
Non Dubbed Grunts: Like other fighting games of the time. Some special introductions are full of dialogue (and sometimes even Mythology Gags) that are completely incomprehensible if you don't understand Japanese. Special post-battle victory banter text were dropped in the overseas versions similar to what happened in the Street Fighter Alpha games.
Sakura, thanks to the magic of recycled Alpha sprites.
Pet the Dog: Balrog's ending has him donating his reward money to a charity.
Please Put Some Clothes On: Maki. Surprisingly, Mai, the one character who is notorious about this (and whom Maki is frequently accused of being modeled after in terms of appearance), gets away without so much as a peep.
Surprisingly Good English: The announcer, radio DJ Hiroaki Asai. If you listen closely, it's clear from his random pausing and inflections that he's not a native speaker of English, but his annunciation is quite good overall and his being a Large Ham Announcer makes up for everything as a whole.
Eagle and even Zangief don't sound particularly Engrishy. Raiden is a special case in that he actual is voiced by a native English speaker (John Hulaton), but sometimes doesn't sound like such due to the voice direction.
Took a Level in Badass: Ryuhaku Todoh was basically a Joke Character in Art of Fighting with only one special attack. It took the efforts of daughter Kasumi in sequels and then his big return in this game to show just how badass the Todoh Style can be.
Unexpected Character: While a few character choices are no-brainers (Rock, Haohmaru, Athena), others are more of the "Wait, what?!" variety (Chang, Eagle, Hibiki, Kyosuke, Maki).
And then there's Ryuhaku Todoh, a character whose mostly been a background cameo as a Running Gag after his first playable appearance, way back in the original Art of Fighting. Capcom vs. SNK 2 marks the second game in which he's playable.
Updated Re-release: Capcom vs. SNK 2 EO, with many tweaks, and two new groove choices. The GameCube version dropped online multiplayer though and is the only console version (aside from the Western PS2 releases) without it.