Peco: As they reveal themselves as Yggdrasil during the end game, it can be assumed that the Mutant and Peco are one and the same person. Clues are Peco's anger in their first appearance as something went wrong and their frustrated expression towards Momo's explaination. Another clue are the voices the party heard near at the Yggdrasil tree, as they found Peco there after reuniting with Momo.
In the same vein, Peco may have feigned stupidity first to resign themselves to their new fate, another reason may have been later to fool Myria, in order to catch her offguard.
Myria: Is she a totalitarian bitch who just wants to control humanity, or a Well-Intentioned Extremist who has spent her life working to protect humanity from the Brood? It doesn't help that the game heavily implies that Myria is actually the same goddess Bigger Bad Myria from the first Breath of Fire, making the idea that she's genuinely altruistic that just much harder to swallow.
Awesome Art: All sprites are hand drawn, with an insane amount of detail and commitment to making every frame on model but expressive. This is generally considered one of the game's better points.
Broken Base: Is the jazz-styled soundtrack a cool and unique break from the common orchestra or rock soundtracks of JRPG's, or is it ill-fitting, boring and just downright grating?
"Funny Aneurysm" Moment: The revelation that Momo's father used to conduct experiments on chrysm ore in order to resurrect his dead wife; it makes the sight gag of finding his Porn Stash a little unsettling.
Sidetracked by the Gold Saucer: Fishing, especially now that the game introduces Manillo merchants, who offer awesome rewards in exchange for fish that function as Disc One Nukes. note The first example being the merchant west of the Farm, who sells the Silver Knife, a weapon that will make the Bosses in the McNeil Manor complete jokes, in exchange for fish that can be found and caught with ease in the first two fishing spots.
Woolseyism: Some of the Dub Name Changes fall into this: The lumberjack Babadel was renamed like legendary lumberjack Paul Bunyan, the traitorous Zurusuru was renamed like the Norse Mythology's god Loki, the generic-named Great Wise Tree and Dragon God were given mythological upgrades into Yggdrasil and Ladon and the crystal/fossil pieces found around were switched from "Ghost" to "Chrysm".