With “Limited Freeform” magic, it seems that magic would be the skill of choice since it could easily substitute for any other skill. With the right group, you might avoid that. Did this cause any problems in the games you were in? Did anyone express concerns they had “wasted” their top slot for a substandard skill?
I'm not Joel, but I'll answer this anyway, since I ran the game and use a similar magic system in my own fantasy FATE game.
The short answer: No, it's fine.
The long answer: Magic can't really substitute for every other skill by default -- you're limited by the special effects of what your magic can do. For example, Joel's air-and-beast mage (an odd combo, I'll admit) couldn't use his air magic to be persuasive in a conversation, or use his beast magic to read an ancient language. He'd still use Rapport and Academics for those.
Another balancing factor is the virtual necessity to take certain penalties to your magic-related skill rolls -- for example, to target multiple enemies or attack them at range -- which probably means spending Fate Points to bolster your odds of success. You're welcome to blow all your Fate Points on a giant fireball or something, but it'll also mean being subjected to more aspect compels to earn those Fate Points back.
In practice, I haven't seen spellcasters dominate non-spellcasters in any significant way.