I feel like the issue was one of Flavor, especially in the case of BLU. Blue Mages were known for using enemy skills and learning them from the selfsame enemies. Which is a troublesome task to adapt, and so skip out on one of them would mean losing its general flavor...

As such the devs decided that fidelity was more important that balance. the "lack" of which is inherent to Blue Mages due to their versatility and access to spells like White Wind and in certain games, (Bravely Default namely) the most powerful elemental magic).

With that said The issue with Beast/Puppetmaster is a different one that might have the same result as Blue Mage, that being how the devs handled pets. And even then a MCH-like workaround might suffice by having them only be visual indicators.