Another great boss that I come across at first wasnt a foe,not even a threat at all.He is High Priest Zera,the somewhat pope of the Granas religion which most people in the game believe in.
Yeah, Zera was pretty cool as an end boss. Nacho must be a lot more perceptive than I am, because Zera's betrayal came from completely out of left field for me. I hated him more for the fact that he "killed" Millennia, who has to be one of my all-time favorite heroines.
Other favorites: Anubis/Nohman from Zone of the Enders II: The Second Runner, and Cubia from .hack//GU.
Anubis makes his first appearance right at the very end of the first ZOE as an unbeatable boss, then shows up again early in ZOE II and completely wipes the floor with your ass. By the end of the second game, you're completely psyched up to face him, and then he delivers with one of the most insanely intense boss battles in any mecha game in history. Anubis vs Jehuty is like a mecha version of Goku vs Vegeta, with energy blasts flying in every direction, both mechs teleporting around the battlefield, locking blades in melee combat, and utterly destroying the battlefield. Good times, good times.
Cubia wasn't such a great boss because of his entrance in GU Volume 3; it was kinda "Surprise! Here I am with only the most tenuous connections to the plot of the previous two games!" but it was nice to finally get some closure with the big lug since you couldn't really kill him in the original quartet. One awesome avatar battle with Haseo wielding the Key of Twilight later, you and your selected party attack the core in another of the most insanely intense battles in RP history.
Cubia never stops spawning Gomoras for you to deal with while you try to kill off his two arms, which retract out of attack range and lengthen the battle significantly before the core itself comes into range. The music is some of the best around, the action is frantic and altogether epic, and the ending is incredibly satisfying to boot.