Vagrant Story is definitely a flawed conception. Narratively and cinematically it's absolutely top tier. I could hardly believe it was a PS1 game with its presentation. Its cutscenes -- rendered completely in the in-game engine -- are seriously movie quality. The art style allows its graphics to be fairly ageless, and the direction, lighting, and facial expressions are seriously impressive.
Mechanically, it's a mixed bag. It doesn't provide any tutorials, and what little it does tell you is often incorrect or contradictory.
I only felt like I completely understood the combat toward the end of the game, to be honest, which is definitely a rather glaring flaw. Once I did understand exactly how it worked, and how to exploit it, it became really easy, but early on I definitely felt overwhelmed, even reading FAQs about it.
Unfortunately, no amount of learning or trial-and-error will help with the really convoluted menu system. Even binding the Quick Menu to something easier on my Vita, the amount of digging around you have to do to change or reassemble weapons/gems is tedious as hell.
Ultimately I think it's a game that would benefit astonishingly from a remaster. It doesn't need much more than some polish aesthetically, IMO, but there's so many facets of gameplay and navigation that could be fixed with the simplest of changes. Like:
There needs to be a hotkey for weapon swapping. Menus need to be far more responsive and streamlined to cut the tedium from inventory management. A simple directional compass would significantly improve the minimap and prevent constant map-checking. Having each room's name pop up or be labeled somewhere on the UI would also ease exploration. Frankly, I wouldn't mind if they turned it into a straight Crisis Core type combat system for mass appeal.