The Neo Geo's big problem as I recall, was that SNK simply took to beating the crap out of sequelizing their fighting-game series--Fatal Fury, World Heroes, Art Of Fighting, King Of Fighters--to death, and in retrospect, very few people really care for those much, right? Only Samurai Shodown really seems to be regarded as a classic (and I'm just now finding out it too had ten zillion sequels.) So if you wanted to play dozens of different SF2 ripoffs, Neo-Geo it was.
When EGM did a Top 100 All-Time games list in the late 90s, Gunstar Heroes was the highest ranking Genesis game on the list, at something like #27. The letters section they received in the next issue complained about the overuse of Nintendo/Mario/Zelda stuff in the top 25 or so quite a bit.