I think people forget that this game is essentially a fighting game. It's not meant to have a KH-esque story. The story in the original Dissidia was a huge leap ahead of most fighting games in terms of storytelling and 'plot'.
It succeeded in what it set out to be; a crossover fighting game that sparked nostalgia for fanservice. Kefka with his insanity, Golbez with his brooding cryptic dialogue, Emporer Mateus and his grandiose delusions, Exdeath and his 'void, void, void, also void' shit, Terra's self-doubt and demure attitude. Even under developed characters had what little information given about them fleshed out, Firion's hot-blooded love for freedom, Garland's obsession with destiny and the circle of time.
I really don't know what more people could have asked for. Some people complaied about the Amano influence, but it was actually a fair trade off. All of the characters that were defined in higher detail (FF7+) looked exactly spot on. Low-res era characters were recreated wonderfully, and exactly how I would imagine them to look had FF1-6 been made 10 years later..
The combat system was new and interesting. Nomura set out to make a game that played 'like the fight scenes in Advent Children' and succeeded. Had they made the game more conventional people would have complained that 'This is just Street Fighter/Tekken/Soul Calibur/Smash Bros. with Final Fantasy characters!! SNORE!!'.
Call me a Dissidia fanboy if you want, but I loved the original and plugged in 160+ hours into my file.