Got it working! Another issue, after editing the fba2x config file to map another button configuration for keyboard or joystick, the changes aren't recognized and Pifba keeps the same button configuration.
I have the Retropie SNES basic configuration for joystick. Tested with "jstest /dev/input/js0" command. And i am running Pifba from the Retropie Frontend with "./fba2x ROM".
Marvel vs Capcom 2 is not supported?