For the sake of the argument, i wont mention which company, division or sub-division made what (same way Arc Systems works for Sammy, SNK also has Noise Factory and so on):
Better overall presentation (from animation to sprite quality to music). They used to make just gorgeous, gorgeous games where everything would fit together… no mis-matched sprites, no mis-matched animations and so on. Their games seemed more like “experiences” than actual competitive games. Most of their stuff was just plain broken. Besides KOF98, Garou, RB2 and FFS, they didnt have much for serious play.
Started dissapointing, but its now doing pretty good.
KOF2001 and 2002 are the ugliest KOFs ever. 2001 is just a shitty game overall, while 2002 plays great. SS5 and SS5s, like 2002, look ugly but play great. SVC sucked, KOF2003 was good. KOF2001, 2002 and SVC also suffer from awful music.
But right now… ignoring the fucking annoying rehash issue (at least they still make new sprites - NGBC has like 12 new ones), their games are good. NeoWave, KOF:MI, NGBC, KOFXI, SSTenka - they all are or seem decent. The backgrounds and music are MUCH better than the 2001-2003 years (hell, i would say the backgrounds are better than anything theyve EVER done - just look at this, this and this.), and theyre taking more chances with gameplay (see NGBC, KOFXIs extra bars and systems, all the grooves in SSTenka).
They also seem much more concerned with testing and balancing the games than SNK ever did back in the day (MI excluded, being a console game).
On the issues of graphics, you can only expect any investiment in the 3D games, though (MI2 for the XBox360 will be a big investiment for SNKP).