Anticlimax Boss: Amon, especially when compared to Gades. This is explained in-universe: Amon, as a God of Chaos, exerts his power by causing chaos in other people and remaining behind the scenes himself, while in actual hand-to-hand combat he's a pushover.
Broken Base: The new designs for the characters. Some players find them okay, fitting for a remake of an older game and giving something new that was created for the changed environment of the game. Some players find them horrible, as they 'Squarified' the characters, making them all appear younger and hating more extreme changes like Iris going from a black clothes theme to a Woman in White or changing Tia from a demure, gentle young lady into Rita Mordio. Here's a quick comparison.◊
That One Boss: Every fight with Gades. In his initial, human-sized form, he's lightning fast and loves to use Teleport Spam, so it's difficult to even get a hit in on him before he's dealing out yet another attack. As a giant, he hits like a truck, has mounds of HP, leaves very few opportunities to attack his weakpoint, and to top it all off must be beaten multiple times in this form. By the time he shows up on Doom Island, the party should be strong enough to take him, but his appearance there does come as a surprise to unwary players.
They Changed It, Now It Sucks: Most of the complaints are because of the Mons system (which added, from a handful of choices, a seventh, CPU-controlled, beast NPC on your side), which was in the original game but removed in the remake, and how much of the old game's sidequests, locations (we're talking about a BIG part of the world map) and characters, even villains, were axed from the DS version.