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.
Complete Monster: Bishop Ladja, despite only being The Dragon, becomes one of the vilest characters in the series in the DS remake. He specializes in committing an even more horrific atrocity than his last in most of his appearances. His first scene alone has him brutally beating the hero and Harry (who are six years old at the time) to within an inch of their lives, laughing sadistically all the while. Then, when the hero's father, Pankraz, arrives to save the day, he threatens to murder the hero if Pankraz tries to fight back against his enforcers. After the enforcers are done beating him, Ladja coldly finishes off the dying Pankraz with a giant fireball, then carts the hero and Harry off to a brutal slave labor camp for over ten years. He's also at least somewhat successful at being The Starscream, killing off one person ahead of him (King Korol) in the chain of command for the power. Finally, he makes sure to wait until the main character reunites with his mother (after over 18 years apart) to kill said mother, just for maximum emotional impact.
Ensemble Darkhorse: The only reason why Ladja becomes so much more important in the remake is because of how popular he was. To a far lesser extent, Dwight "Da White" Dwarf also goes from a memorable Warmup Boss from the beginning of the game to a full fledged party member.
Prince Harry is also very popular for a Guest Star Party Member, with many wanting to see a version where he permanently joins the team and others wanting him to serve as a Gay Option.
You can't forget Tuppence either, who goes from a completely random recruitable generic soldier with weird hair to a wisecracking Casanova Wannabe.
Game Breaker: In the SNES version, it was apparently possible to hit nothing but criticals and automatically recruit any suitable monster, by giving your hero very specific items (and nothing else, reducing his combat ability). Somewhat lessened by the fact that one of the items is only available very late-game.
Hilarious in Hindsight: One of the nuns in the Heaven's Above Abbey says, "I'm sure there will never again come a time when you are forced to submit to the will of another." Marry Debora, and you have this trope in spades.
Combine that with Name's the Same: In the 1997 manga adaptation, the Hero's daughter is named Sora (or "Sky"). And that is five years before Kingdom Hearts, where that name belongs not to a girl, but rather to a boy with the Keyblade. Also, that manga was created over a decade before the DS remake, when she and Ten (or "Heaven") had their Canon Names changed to "Madchen" and "Parry".
To wit: Using the hero as a human shield in order to prevent Pankraz from fighting back against his flunkies, incinerating him with a fireball after said flunkies had already beaten him to within an inch of his life, carting the hero and Harry off to a slave camp for the Religion of Evil for ten years; and then, much later on, turning the hero and his wife into statues for eight/ten years (the hero was freed eight years later, and it took two more years to find the wife).
In the DS version, he doesn't die at Talon Tower like he did in the SNES version. He goes on to show up near the start of the final dungeon, where he blasts Mada — the hero's mother and the woman you've been looking for the entire game — with the same Giant Instant Death Fireball of Doom that killed Pankraz, within seconds of finally seeing her, forcing one more boss fight with him. Fortunately, this doesn't actually kill her. Unfortunately, Grandmaster Nimzo finishes the job.
Purity Sue: In any other game, Nera would be this. Absolutely everyone she comes into contact with, including an abbey of nuns that mention they've learned more from her than she did from them, can't help but talk about how beautiful and pure she is. Despite this, the game heavily suggests you marry Bianca rather than Nera.
Rescued from the Scrappy Heap: Nera goes from a worthless party member who makes Bianca's life terrible in the original version to a completely viable romance option who doesn't completely ruin the Whitaker family if chosen in the remake.
They Wasted A Perfectly Good Charater: Ladja in the original game, with his initial Moral Event Horizon when he first appears seem like a great way to set him up as a major villain, but he ends up being nothing more than a flunky for King Korol, whose actions have far less of an emotional impact on the player.
Sancho's heavily stereotyped accent in the DS translation is rather... unfortunate, particularly given his role.
You can equip your 8-year old daughter with a lacy bustier, a silk bustier, the dancer's costume, etc.
The Woobie: This game is filled with characters you just want to comfort. The hero, Prince Harry post-breaking, Bianca, Nera and Debora as the bride, your pet sabrecat, Sancho, the twins... And that's without getting into all the NPCs you see broken and hurting throughout the game.
Woolseyism: Almost everything has been renamed in the English localization. If you don't dig the Punny Names and the Narm Charm of the localization, this game will be a Macekre for you. Especially if you've already played the much more faithful fan translation of the original SNES game.