The first thing it does well, right out of the gate, is present a unique, beautiful setting that's exceptionally nice to look at and listen to. Then you're hit with the voice acting, and it really helps sell the fact that this game was unlike anything else that was released at the time. The sprites are absolutely gorgous, and unlike most games in the genre, at least around that time period, your protagonist was a female, who begins to question her role, and not a typical JRPG hero.
The second thing it did right was present some of the most absolute heartbreaking moments in gaming. Some characters you catch glimpses of before you recruit them, some are brave, some are scared, some heroes, other villains, but they're all gonna end up the same way if they're joining you. Seeing the pieces fit is where most of the story is.
The game's primary flaw was the way the difficulty presented. Easy is harder than Normal and Hard due to the lack of time to train, and making the endgame bosses almost impossible to beat, Hard was better for min-maxing. Also, the endings were too frustrating to ever get without a guide, but those are relatively minor complaints about an otherwise astounding game.
It's a game that you generally have to use tactics for. Lezard's Tower is easily one of the game's hardest dungeons, due to its size, and puzzles, as well as difficult battles. Getting the right party out, using magic correctly, and making good use of item creation solves many of those issues those. Save Scumming is also useful in deciding which areas to tackle when, but most everything is beatable, even if a perfect run is nigh impossible. The random element may have hurt you, due to some areas opening up earlier or later, meaning you were less prepared, but everything's beatable for the most part.
Also, the game has some astounding antagonist's (tri-Ace's specialty, it seems).