Would it have also helped to have given your ape four gems--2 for the spell cost, 1 for the level gain, and 1 more for fatigue reduction? That seems much more convenient than having to spend multiple turns forging an item and getting the mage to a lab to equip it, just so he will feel comfortable about casting one spell that he could have cast anyway if he weren't so worried about losing consciousness. And presumably it would work with Storm Power too.
I agree though, it's lame that such an obviously good spell choice would be overriden by a commander who should know better. The spells in this game are so varied and quirky, it seems very natural that big, special-effects like universal flight should get their own special priority determination methods (and maybe they do). For instance if Mass Flight was always given a priority boost when a large enemy army could be seen beyond a wall, then maybe that would overcome the excessive fatigue penalty. Or maybe the excessive fatigue penalty should be reduced when the friendly army is very large (thus meaning the tired-out mage won't be lying unconscious on a battlefield all by himself). And maybe it is, how would I know?
There are so many details that could go into their spell-scoring system--how interesting that code may be!