It could have used some tweaking (and it was eventually for Trials of Mana) but it works well as it is now, and is already enhanced when compared to its predecessor, Mystic Quest/Final Fantasy Adventure. It's basically this game's equivalent to turn-based combat, merged with top-down Zelda-style combat, and if you think of it like that it all makes sense. The attack animations feel off and enemies don't really react to being hit the way you'd expect them to, but you get used to it. It's hard to get into at the start because the combat is immediately quite awkward. You would think the game would suffer over this but it still holds up surprisingly well.
This is all to be expected just by knowing the backstory of the game, being that 40% of its content had to be scrapped in order to fit the game into a 32mgb cartridge. One thing that happens a lot too is that the music gets cut off by sound effects and that's really annoying because a lot of the music is amazing. There's also not really an ending, the game just cuts to the credits after one short scene after the final boss. It also has shortcomings in the story, where the translation is off, and the dialogue is structured really bizarrely. While playing, I ran into several glitches, whether that be the UI bugging out, the characters dropping commands randomly, and AI controlled party members getting stuck in geometry a lot of the time. Secret of Mana is definitely an unfinished game.