I've got most of the Japanese PS2 Neo-Geo collection titles, and I have to say that they're all pretty close, if not identical to the MVS originals.
The KoF Orochi Collection (KoF's 95 - 97) features all three original titles in what I would call a nigh on perfect set of ports. Certainly if there are any differences, they're so small as to say un-noticeable. The cool thing with these ports is you can either play the original cart OST, or choose the NeoCD arrange OST's.
KoF '98 Ultimate Match does feature the original KoF '98 and it's a perfect straight port.
KoF Nests Collection (KoF's 99 - 01) feature original ports as well as the arrange modes from the DC versions.
AoF collection is a straight set of ports, as is the Sunsoft Collection and Fuun Collection (Kizuna & Savage Reign)
The Last Blade ports are not quite there, but only just. The graphics and sound are fine but the difficulty on LB2 is well off, making it very challenging, especially to a casual player like myself. I certainly don't recall my AES copies being so difficult on the "easier" settings.
Not got Garou MotW, World Heroes Collection, ADK: Tamashii (yet) or the Samurai Spirits Collection (yet), but I haven't heard anything negative about them.
Overall, in my opinion the Japanese versions are all well worth picking up and are ideal substitutes for the MVS/AES originals.