This sound a little weird, so please bear with me.
Capcom vs SNK 2 and Capcom vs SNK 2 EO have various changes.
For competitive play, the definitive version is the PS2 version. This is because it is very similar to the arcade version and does not feature any major system mechanic or gameplay changes. When EO was released certain characters had their values altered and changed along with major system mechanics changes.
With the advent of netplay for these old games, ps2 netplay is not all that great while Dolphin is amazing. But because of the differences between the two versions of the game, netplaying CVS2EO does not set up good habits for competitive play in tournaments or arcades.
The file structure between both games are similar but I am unable to discern where what files contain what. There are multiple .AFS files, where the first two are predominately all audio and the third one has various types of files. Trying to use the PS2 ASF02 into the GC results in a hard crash. I can easily extract files from a AFS file, however, I cannot import files with ease. https://imgur.com/a/cspWppQ
is an album of the ISOs file structure.
I'm uncertain for all the changes but the major ones include:
Characters - certain character received across the board health and damage nerfs
System mechanics - A technique called "roll cancelling" was removed