I remember reading up on some of the mechanics for certain things in-game and they come across as completely arcane.
(And I'm not talking about the Battle Mechanics. Mostly stuff regarding Data and other in-game events.)
Oh yeah, there's some weird stuff hidden and semi-hidden in the game. It's pretty common of PS1-era RPGs - everyone wanted cool hidden characters and content, and publishers were more than happy to comply and sell you the associated strategy guides.
For Frontier specifically, the first one that comes to mind is recruiting Suzaku. If I remember right, you had to do:
-Defeat a specific enemy on one screen during the Shield Card quest. It's just some random fairy, no indication that it's important in any way.
-Then run two screens or so over, and see if a snowman has spawned in. If not, you have to go back and fight the fairy again. Note that it has to be a snowman on the BOTTOM of the screen. A snowman can also spawn in elsewhere on the screen. It is the wrong snowman. Bad snowman!
-When you do get the right snowman, you touch it and fight a mini-boss, who is significantly harder than the actual boss of the Shield Card quest.
-If you defeat the snowman, you then have to find a hidden passage in an entirely different part of the dungeon, away from the snowman or the fairy. In there is Suzaku, who will be unfrozen and ready to join you! He's not terribly unique or better than most of the other monster recruits. Enjoy!
This is the one where the super hero's scenario was like half finished... right?
Red is actually more "finished" than most of the characters. I'd personally rank the finished-ness of the quests as (most to least) Red, T260, Riki, Asellus, Blue, Emelia, Lute, though it's possible Lute is intended to be very minimal in story.
That being said the game as a whole had varying levels of completeness, and we don't know a lot of what was intended. Most of the data left on disc was for Asellus's quest, and that seems to be the bulk of what's being restored here (besides Fuse).