2 reasons.
1) Cart Size. Apparently anyting arround 700mb is approaching the limits of a Neo cart's capacity. Smoother animation requires more memory, as do larger sprites. So you could'nt have a KoF-size character selection (40+) with MOTW-quality animation.
2) Development costs. It simply costs more money to draw more animation frames, and we all know that SNK's finances were none to healthy back in 1999.
Imagine how muh it would cost them to re-draw 40+ characters in MOTW style. I'm not sure SNK (or Playmore) could afford to do that all at once.