You got your answer the moment you played MUGEN.
Spoiler, click to toggle visibiltyEx: Try MKX Raiden vs MK1 Raiden. MKX Raiden will destroy MK1. Order Sol vs MBison. Order Sol will crush M. Bison(MvC) out of the ball park.
Now the KOF systems are not THAT different, so you may have a better competitive match there. KOFXIII should destroy KOF 02, system wise.
plus you have to play test every character for the smallest detail to see if you can cheese a victory,
Like Doa vs VF, Doa will win, Reason? annoying counter hold.