There's a difference between the job system and systems VI and later used, at least for me. When I used the job system, I made my party different. In III this is pretty much a given, seeing as you can't mix jobs (part of the reason I love III's job system) and in V making characters exact copies in terms of abilities would be kind of foolish. I always only played for story and stuff so I never bothered mastering all jobs in V after I beat the game, ending up with characters that were all very different from each other. Same as in III, my party members each were very different from each other (okay, I am training for a party of 4 Onion Knights in III DS but that's just to kick the IG's behind for fun).
In VIII for example (A game I really like, mind you, but I do not really like character clones) I never felt the urge to make my party different cause there's barely a reason to. The balance in VIII is so off that it didn't need a balanced (different) party like in III or V. And in the end, I ended u pwith characters that were all junctionned the same and had the same abilities (magic, GF and Item/Draw). Ultima junctionned to strength, strong healing magic to HP and so forth. You know it makes your party walking demi-gods and there's not a single situation in the game that requires you to do it differently. Ending up with copies.
The same I prety much had in VI for example. Everybody can learn magic. Then why shouldn't I learn them? The game pretty much urges you to do that (I'm not a challenge player either), ending up with copies, again. In V everybody can use all magic as well, true. But wait, magic in V was still devided into numerous types. In VI there is one list of magic. There's no ability 'Time Magic' or 'White Magic' like in V. The clone-stuff in VI wasn't that hard however, for characters still had pretty unique abilities themselves. (Wonderful, I said something positive about VI
-_- )
In VII this fell away. Your characters are empty and you can fill them up however you want (like in III and V, agreed). It was still bearable in VII for me, because there's so much different Materia. This was no longer the case in VIII, like I said.
It's the worst in XII though. There really is no reason to not equip your characters with the best stuff because magic is not that usefull in XII again resulting in total copies.
With a job system, this is not that possible, because not every job has access to everything, like in VIII with junctionning or XII with licenses (the worst games when it comes to clones, however still great games regardless of that, unlike...). A white mage in V for example, can not perfom black, summon, blue and time magic at the same time. In XII this is very possible, and in VIII as well. Even if you have mimes in V, you can still only have 3 types of magic at your disposal at the same time. If you want to use all magic in the game that there is to use, you'll have to give your characters different abilities, thus making them different.
A long rant for just this: a job system never made me make exact copies, VI, VIII and XII did.




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