Ass Pull: Meracle just happens to have the Unobtanium necessary for the crew to escape the alternate Earth with no mention or foreshadowing right up until the very moment.
Broken Base: Is this game a step up from Star Ocean 3 in terms of gameplay and story with no pointless and convoluted plot twist? Or is it a complete disaster with horrendous and unlikeable characters and worse voice acting than the PS1 games?
Faux Symbolism: The Grigori have an angel motif going on: They're all named after fallen angels from the book of Enoch (who were also called the Grigori), the energy they emit as they transform takes the shape of an angel, and the transformed Grigori all have wings, or a wing of some kind. The angel motif culminates with the final boss Satanail, the Grigori with the most angelic appearance.
Narm: The scene after the alternate Earth is destroyed, in part, due to Edge's actions. The scene is supposed to be extremely sad and depressing, triggering Edge's Heroic B.S.O.D., but due to the cheesy voice acting and him generally being a Large Ham, it comes off as unintentionally hilarious.
You won't find many fans of Sarah and Lymle because some fans are turned away by their voice acting and how Sarah is Too Dumb to Live.
You'd be hard pressed to find many fans of this games version of Welch, with many seeing her as incredibly obnoxious and annoying. This is backed by her bad voice acting and being generally useless to the plot.
Edge also gets a lot of hate during his... tantrum.
Scrappy Mechanic: The bonus board gets some dislike because it gets wiped every time you end a particular playthrough and load a savefile. Sure, this is specifically designed to prevent Save Scumming, but surely there could have been at least a little leeway that could have been programmed in? (I.E. allowing you the choice to keep it if it's been an hour or more since your last save, or something like that?)
That One Level: The Cardianon Mothership. Sure, you get Bachus, but the area is hard to look at, the camera hates you and once you get to the force field area, it becomes a LARGER pain in the ass to navigate through. Add to that several large enemies that can stun lock you, break your bonus board and a general lack of breathing room, it becomes a major slog very quickly.
They Wasted a Perfectly Good Plot: One of the first major plot points is Edge and crew accidentally traveling to an alternate-reality 1950s Earth. The potential opportunities and consequences of this story arc could have been profound - the reality of dimensional travel, exploration of history, and a whole heap of ethical, scientific, and practical concerns - especially after Edge is indirectly responsible for destroying alternate-Earth and the entire human race thanks to his naivete. It really could have fueled an entire game's plot all by itself, or at least provided some powerful character development. Instead, our heroes (plus one party member) return to their own dimension and resume their mission, and the only lasting effect is Edge being a mopey jerk with confidence issues throughout the next major plot arc. Once he's back to normal, the whole alternate Earth might as well never have happened.
Uncanny Valley: The anime-like faces don't emote well. It's made even more uncomfortable by the fact it makes them all look so young. Lymle takes this to a whole new level, due to her Creepy Monotone.
Wangst: Edge's breakdown after the alternate Earth arc, while somewhat understandable, is very over-the-top. Furthermore, what followed was Edge being generally unhelpful and acting like a jerk throughout the Roak arc of the game. As a result, many players got rather irritated at Edge with some labeling that phase of his character as "Emo Edge".