Another tough "favourite in X genre" question...
As much as I had a lot of fun with, and nostalgic fondness for, Fighters from the 16bit cartridge based systems, these days I find that only the NeoGeo titles are still worth playing... so for AES/MVS/NGCD I'd go with Garou Mark of the Wolves and Last Blade 2.
All of Capcoms ports to the Dreamcast are awesome. And on the subject of the Dreamcast; Dead or Alive 2, Soul Callibur, Guilty Gear X, KoF 99 Dream Match, and again Garou and Last Blade 2 are all freakin' amazing. In fact, the Dreamcast is probably my fave system for fighters.
Gotta say though, the current gen (specifically PS4) is nailing it too. The recently released Soul Calibur VI is the best entry in the series since SC2 - a really great game. In terms of more traditional 2d fighters, Arc System Works are going from strength to strength - highly recommend Guilty Gear Xrd and Under-Night In Birth.