For the majority of Neo Geo library there is no difference that effects gameplay. However, there is notable differences in the case of Magician Lord, because the AES and MVS are separate versions.

1. MVS has longer invulnerability times upon gaining control of Elta. This makes sense in the arcades because Elta respawns from where he last died. Whereas the AES version makes you start the stage or guardian boss fight over again. In terms of speedrunning, this helps during some of the guardian boss fights

2. AES version has more health, allowing the possibility of damage shortcuts. There's a shortcut in the first level that saves about 10 seconds, which can't be taken advantage of in the MVS (using stock arcade settings) version.