It's not SE who is stacking the classes, it's the community. One group manages to win a boss fight with a setup and everyone slavishly follows the same setup without trying anything else. And since class stacking is easy, it's usually what ends up being used on any fight.

There is nothing SE can really do to stop the players from stacking classes except for requiring a certain setup, which would just end up in a huge whine wave about our "freedom" being restricted.

There are alternative ways to beat the primals, mixed melee setup for moogle for example, but most people just follow the standard setup "because it works"