Using Extra Mode is just a waste of your quarters. Besides the inability to run, the first two characters in your team get meters that take SO LONG to charge up that it's not even worth it to do it. Plus, the attacks you can use after dodging an attack are pretty slow, and are not comboable like they were in KOF '95. Extra Mode only favors grapplers, but even then characters like Goro and Clark could do more damage with Advanced Mode.
Advanced Mode is the only mode worth playing in KOF '97 and '98. Andin CvS2, we'll be able to prove that this mode is the best one of all, even surpassing the standard Alpha Modes and Parry/Just Defended modes.