I don't see it as very Mary-Sueish to have all three leveled to 50, but that's partly from how I see it. Being level 50 doesn't mean you're the most powerful caster around. It merely means you're very good at its combat applications, to the best that an all-around adventurer can be. Key aspects of this are that you only utilize what has come before you, you're not researching new techniques. You're also relatively untrained in the other aspects such as military strategy or quieting ceremonies. It is the higher ups in your guild that are the true master wizards, so mastering all three is less like being an archmagus with unparalleled mastery of magic, and more akin to a well-traveled explorer who's learned several languages.

Another thing to keep in mind is that it's more than just the soul crystals restricting you from utilizing all three at once. Magic requires more than just the knowledge of how to cast it, you also need the right focus. For a WHM, this is a wooden focus, the more natural the better, for communing with elementals. For a BLM, this is an ornate and expensive focus as befitting the greedy religion of Nald'thal. Finally, for both Arcanist jobs you aren't using the book just to remind yourself. Rather, it's the geometries written in special ink designed for channeling aether that you use, with a book being your medium because it's more handy to carry around than a stick covered with all those designs. With your book in hand, you can only do the most rudimentary conjury and thaumaturgy, the kind that does not require a focus.