There's great romhack called capcom fighting collection, it includes cvs2, mvsc2, sst2, 3rd strike and a couple of others and it's only 800mb. I've tested it and it works fine, even the saves from standalone roms work (i had saves that unlocked all chars in cvs2 and mvsc2). You might take a look at it, cause i don't use naomi version atm and can't help you...I tried it once expecting different performance but it was the same so i ended up using dc version.
You could also convert dc mvsc2 into .chd (if you haven't already), it'll be around 150mb which is not much bigger in size compared to naomi rom.