MOTW, and the two Last Blades, are definitely the best fighters on the Neo Geo.
They have features similar to the SFIII series, for example Just Defend, where you can block an attack (if you get the timing right) and then follow up with an attack of your own. And they have super moves, and the T.O.P. guage, and the Speed/Power modes for the Last Blades.
It's hard to say which is, for me, the best FF game (after MOTW). Probably whichever FF game has the most selectable characters, and also has Geese as a playable character. The FF games, especially the FF3/Real Bout games, are quite similar to each other.
I think the best fighting games are whichever are the best for head-to-head competition between two human players, at a high skill level. So, the best 2D fighters ever made are Last Blade 1 & 2, Mark of the Wolves, and the Street Fighter III series. The parry moves in these games mean there is a lot of potential for skilled players to increase the quality of their play. As far as I know, no 2D fighters before these games had a move to parry/block and retaliate.