-Minor sequence breaking possible, like you can gather the Masamune parts out of order and even keep Ayla for the fight with Magus
-Extra areas and dialogue that flesh out the story more
-Makes 1999 an explorable area - this was really cool at first but it kinda falls apart in a buggy scenario
Mario RPG still holds up for me - it's a really well designed "beginner" rpg, though the platforming is kinda stiff. Even now I'm still impressed by the amount of hidden stuff and the breadcrumbs it teases you with. Still kicking myself to this day for not finding the Casino on my own, when I managed that with most of the other stuff.
Another dick-move of Nintendo was taking down not only Super Mario Royale, but also DMCA Royale (they had replacement graphics ready but Nintendo wasn't impressed). Interestingly enough, Nintendo is about to release almost the exact same idea for Switch.