Hidden Bosses can be used once they have been defeated. The conditions of the Bosses to appear are to fulfill two out of the following three conditions. If you play with a Capcom groove you will get Ultimate Rugal, and if you play with a SNK groove you will get Shin Akuma.

Achieve over 1500 GPS by the end of the game.
Defeat the Middle Boss (Geese or Bison/Vega).
Achieve at least one Finest KO.