This was one I was pondering while I was playing the retranslation last night, and it's probably been covered a hundred times (though I couldn't find it through a search, I'm rather bad with searches), but I was curious about it.
I had just brought Magus into my party and was rather painstakingly trying to get his tech points built up, and kind of complaining to myself about the game device rendering him less of a mage than he had been hours earlier in the game. Then I had a thought regarding it and thought, maybe it wasn't a game device at all.
During the confrontation with Lavos (when Crono was getting killed and all that), Magus confronts Queen Zeal and Lavos, and some sort of electric-looking energy takes hold of him and he says something to the effect of his magic being "drained away". So the thought occurred to me, maybe when Lavos was draining his magic, Magus lost enough of his power that he became unable to perform those higher-level spells, and it was only through the course of battling that he slowly built his magical muscle back up to par, thus the whole part where he has to relearn spells he was easily smiting you with back in 600 AD.
It probably is something that's been decidedly obvious to everyone else here, but I was really proud of myself for thinking of it, heh. What can I say, I'm slow.