AF gear being better than multi-melded crafted gear is well-deserved. The fact that they are job specific isolates them balance-wise from everything else in-game.

The point is, when on the job you will always want the AF gear on - as each part will be the best in slot without dispute - or should be. However, they are limited to being on the job to be able to use, and thus every other gear in game will have it's use as well.