In 1.0 bonus stats were tied to your character rather than class and they had a number of issues with attempting to unify that system with the armoury system. Of course there were several other problems (or features if you like) with character level being separate from class rank and I believe 80%-100% of your stats being chosen by the player (every level you'd get like 4 stats to allocate I think, though things were capped). Class guilds sold items (for guild marks rather than gil) to reallocate stats in bulk, like 40 STR -> 40 INT. I suppose some people like the hassle required to go from playing job X effectively to playing job Y effectively, but that just doesn't seem to be in keeping with the spirit of the game at this point in time.

More to the point of the OP, I assume the system is a relic of what I described above. Personally I think it would be more effective if the bonus stats were secondary rather than main so there was at least some kind of choice. There are at least instances where 2 people with the same gear might make different decisions between crit and determination (and accuracy and skill speed), where they'd both make the same choice for their main stat.