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.
Also agreed, except that's all you get with any character. They are nearly all throw away immediately after you acquire them. In fact, the very nature of the game is to train them and throw them away. Aside from Lucian and Valkyrie, none of the other playable characters get any development. That was a huge letdown for me. Most chapters had very little actual game story either (it was all packed into the end). So, with no story and few characters that meant anything, it made for a pretty boring game after a fantastic intro. It didn't really deliver what it set up.
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.
The whole game needs a guide really. You're basically required to get certain items and skills to have a chance in the game. And you have no idea where they may be. You just have to waste your periods since you are penalized to enter and exit a dungeon, or visit a town. It really kills exploration when you are always penalized for everything you do. You can't afford to exit, heal, and re-enter to look for missed things without potentially sacrificing the ability to enter unexplored dungeons or towns. The Cave of Oblivion was random and could contain nothing and be a complete waste of time. While the idea of limited time was fine in concept, I thought it was poorly executed in the game with not enough periods to play successfully and be fun. (I played on normal.)
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.
The moment you leave the tower and do ANYTHING else (like train, enter a town, etc.), when you re-enter it's impossible to get the good ending. I played to the best of my ability up to that tower and enemies easily killed me. If you leave and train, you get the bad ending. There seemed to be many poor game design choices like this. It seemed to half-baked, and the difficulty ramp looked more like a third order polynominal rather than a ramp!