I've got most of the Neo Geo Online Collection releases and your right, they do vary in quality between releases. Some have filters, some don't. Garou Battle Archives and Fuun Super Tag Battle have 240p, others don't. World Heroes Gorgeous lacks the warping floors of the arcade (interesting because several emulators couldn't do this either).
Still overall they are pretty good representations of the games, and vastly superior to the ones done in the west. Some even added Vs modes for the fighters which didn't exist for the original Neo releases.
Anyway, OT: SS is the best Neo port for Genesis, hands down. It looks extremely similar, and a lot of the various sound FX made it across intact, unlike the Fatal Furies or AOF. I remember being very impressed with the port when I saw it.
All things considered, the MD wasn't really suited to arcade fighting games of the time - it seemed that in most cases an accurate conversion was just out of the machines reach.
The Sega Saturn would see to that though.