The plot has been massively upgraded, giving multiple major villains focus over the course of the game as well as eliminating many "big-lipped alligator moment" tropes present in the N64 version.
There are cutscenes.
Balancing:
Leveling, for both stats as well as elements. No longer do you need 7 points each in Water and Earth to unlock Healing 1.
Monsters, especially on their stats. Some are harder to defeat, and others easier. The elemental weaknesses/strengths have also been modified slightly to make more sense.
Spirits:
Some spirts have been moved into better places.
Some spirits are easier to get to, due to one of the cons below.
Spirits are far easier to see, which can likely be attributed to the fact that they're much bigger-looking and not at 75% transparency.
Game Length:
The game is far longer, due to added cutscenes and plot elements.
You will be spending far less time grinding early on.
GBC Cons:
Colors:
The colors are far too saturated, making the game very difficult to see on a screen that isn't backlit.
The color palettes chosen are somewhat clashing, and not entirely pleasing to look at. That's not to say they're bad, but certainly most game developers would never have chosen that.
Movement Borders:
They're far too thick! It's very hard to tell how far exactly you can move in battle. Does it end when the top of your character's sprite touches the very edge of the border? His feet? I truly can't tell.
The moving lines effect could potentially cause seizures of some kind, especially if you're fast-forwarding in an emulator. In my experience, this effect has given me quite a terrible headache before, and causes me to play less.
Sound:
It's very, very loud.
Some songs are very screechy and grating to listen to.
These are not good conversions of the N64 soundtrack. Not at all.
General:
Want a leveling guide or a spirit location guide? Good luck finding one! I have only found one before and my attempts at finding it just now were futile - I don't think it exists anymore.
The controls are mildly obtuse. It took me far longer than expected to figure out how to cast Healing 1 outside of battle.
Areas feel much smaller and cramped - it feels like they wanted most areas to take up a single screen without some kind of "entryway" scrolling like the Game Boy Zelda games do, and compromised by scaling areas down.
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since i doubled up, or you lost your stack and if i gave it to you instead of running off at the roulette table does that mean i "gave" you a stack lol