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. It's worse considering that Chun-Li got a new sprite based off her appearance in Street Fighter III: Third Strike. Ditto with Eagle, Maki, Yun and Kyosuke getting new sprites as well. Granted, Yun would have only been the only one of the bunch who would have made sense; Eagle only had his Street Fighter sprites, Maki from Final Fight 2, and Kyosuke from the 3D-only Rival Schools — all of them would clash horribly with the in-game graphics.
Battle Amongst the Flames: The Osaka stage where you fight God Rugal or Shin Akuma is set against a backdrop of the rest of Osaka burning down.
Battle in the Rain: The Osaka stage where you fight unpowered Rugal or Akuma is set on the roof of a temple in the middle of a thunderstorm.
Bonus Boss: Bison and Geese. They were originally final bosses form the previous installment. This time, they are mid-bosses who interrupt you without cutscene. Looks like they want payback from the lat encounter. Fortunately, they aren't modified-for-CPU unlike before as they play the same technical rules.
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, which, again, was replaced 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 characters receive access to a Super Move once it's full but the MAX state 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 2001 became Mark of the Millennium 2001 when it was ported overseas, though the announcer still says "Millionaire Fighting 2001!" at certain points on the character select screen.
Multiple Endings: Occurs depending on the player's performance. Three possible endings can occur while the player character/s celebrate winning the tournament in Osaka:
The celebration is uninterrupted, as the camera zooms out of the stadium to a shot of Akuma or Rugal's foot.
Akuma or Rugal interrupts the celebration, demanding a match against the winners on top of Osaka Castle. If the player wins, they comment on their strength before challenging their true rival (the other boss), as a large explosion occurs. The fates of everyone are left unknown.
The celebration is interrupted by the fight between Akuma and Rugal. Depending on the player's score, one of two scenes play. In one, Akuma mortally wounds Rugal, only for the latter to infuse his Orochi force into Akuma, who is driven insane by the power and turns into Shin Akuma. In the other, Rugal kills Akuma and absorbs the Satsui no Hadou from his body (his special intro has him throwing away Akuma's corpse), transforming into God/Ultimate Rugal. The winning team goes on to fight the bosses in the Osaka Ruins. Defeating Shin Akuma has him being swept into the sky by the Orochi force while Ultimate Rugal's defeat results in Akuma possessing Rugal's body, turning it into his own, before walking away. The following news coverage depicts Osaka being rebuilt, the critical reception to the tournament, and the (text-only) fates of the champions.
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.
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.
Shaggy Dog Story: Some of the character endings turn into this. Maki never finds Guy, Mai never finds Andy (nor does she trick him into marrying her), Rolento doesn't find anyone to join his army, Balrog wins the prize money, but accidentally gives it to charity, etc.
SNK Boss/True Final Boss: Predictably, Shin Akuma and God Rugal. The first is Akuma being given Rugal's Orochi power while the latter is Rugal taking the Satsui no Hado. Getting to them is one challenge (See Requirements). Fighting them, on the other hand, well... good luck. As much as they follow the same rules of regular play (aka unmodified-for-CPU and the same very-low health), it's AI has a brain of its own... even in the easiest setting (console-only).
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.
Surprisingly, Cammy loses this from the first game due to the switch in voice actors.
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.