Hehe... yeah, I didn't design the system, it's player-designed, so I *know* there are going to be balance issues. And, yes, the Quincy, Augmented Human, and Shinigami class will share a lot of the same abilities, because they're mutually exclusive; a Quincy is a special type of Augmented Human, but you must be born into it... and Shinigami aren't human, by definition, they're souls. (Although Ichigo is an exception. A very, very big exception.) In fact, the Augmented human is probably based off the Shinigami, but, since they can't access certain abilities, like shunpo, they need other things, in place.
The other thing about the shinigami; they're incredibly easy to customize. In the source material, most shinigami share only a few basic traits; most of their abilities and skills are unique to them, and bound to their sword. This is reflected in the insane number of feats they gain, as they progress. The sample characters, a second document, in the thread this is found in, shows how the system can be used to create some of the characters from the show, and quite accurately. It's also, really, not intended to be perfectly balanced; shinigami are to augmented humans and Quincy what wizards are to sorcerers... highly trained and skilled, as opposed to guys who just discovered their abilities by luck, or natural aptitude.
I'd *love* to run it in another system, except there's one problem; I don't know any systems besides d20, nor do I have a convenient rules conversion on hand for another system I don't know. =P
In short, you're not supposed to multi-class, only take a prestige class... and even then, the requirements are extremely restrictive, to the point of, "Only if the DM wants you to have it."
EDIT: Yeah, I agree... they really do get the short end of the stick. I'd say they were more fair, if their weapon did more damage than anyone... but it actually does very little, as much as the spellcaster shinigami's weapon. Their one advantage is the series is mobility; Ishida is routinely shown dodging, constantly... but the charge system seems to shoot that in the foot. I think they were designed earlier in the process, and haven't been revamped, yet, leading them to be in the vastly underpowered stage, right now. I'll have to do some thinking on ways to eliminate that charge system, yet still keep their flavor... maybe down to "Uses per day/encounter/at will" on their abilities.