These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
If you take all the dialogue trees as being in-character for Byuu, it becomes apparent that he's a two-faced manipulative Jerk Ass who toys with the emotions of those around him for fun. He has no objection to torturing suspects, and happily hires assassins to take out his "friends" just to amuse himself. He's a sociopathic recluse who cares for nothing except his dragons, and maybe Frederica. He also steals mushrooms!
Princess Yoyo. Is she simply a naive, inexperienced, yet nice woman who just happened to get tangled in an unfortunate Love Dodecahedron or is it something else? The narrative seems to lean toward the latter. However, portions of the fanbase often picture her a selfish, two-timing slut, among other things.
Fan-Preferred Couple: The Japanese fans ship Byuu and Frederica despite there being little evidence, and Byuu and Yoyo, who broke up in-game.
Game Breaker: You can feed the dragons items to power them up and give them new forms. One of Salamander's forms is called Phoenix, and it is literally invulnerable. Just give it the command Go, and it will destroy every enemy on the map for you while you sit on the sidelines. (Technically, since dragons in Bahamut Lagoon are linked to a unit of soldiers, it's still possible for Salamander's final form to be beaten indirectly if his soldiers are all killed... but as a practical matter, you can just hide them in the corner of the map while your invincible dragon kills everything for you. And the AI isn't smart enough to take advantage of this.)
Princess Yoyo (see Alternate Character Interpretation above), with many of the feelings of dislike stemming from what some have perceived as one of the earliest cases of NTR in video games (i.e. the resolution of her romantic subplot, especially when the player has responded positively in the flashback sequence with Byuu and Yoyo).
Palpaleos occasional gets this as well, mostly due to association with the above.
Ugly Cute: They were aiming for a Moogle-like Ridiculously Cute Critter (might have even been moogles at one stage in development), but the Minidevils were more this, judging by their artwork.