You make the Jobs unique by simply giving them a signature playstyle/concept to that Job regardless of the role they're categorised under. So far they've got it right with NIN (vs MNK/DRG), SMN (vs BLM), SCH (vs WHM), and even MCH to an extent (vs BRD; if BRD never got WM the difference would be more apparent). With DRK, Dark Arts does just about enough whilst AST simply got the misfortune of being designed and promoted as a substitute WHM/SCH-type rather than being given its own core identity to build the Job around.

Now within the roles themselves you may see see a few similarities across the Jobs therein (like melee always having positional based attacks, Tanks having similar defensive CDs) but as long as the overall playstyle and feel of the Job is different then such similarities won't matter too much in the long run.