No matter the game and how you balance it. There always gonna be meta.
FFXIV is overbalanced in many cases. That annoys people a lot. Like in pve all jobs got almost the same skill kit.

The only way to avoid in PVP things like "everyone plays the same combination of characters because it is the strongest" - is to make all jobs do pretty much the same thing.
Do you really want that? I would rather look for ways to deal with that kind of combination. Like having specific players in your party to do the same thing or just insta-kill the annoying players as samurai or something.

In the current meta you can pretty much always find a way how to counter something specific.