Jeremy Irons could be a magnificent Magus, but at 60 years old, he could be too old to play Magus. His voice, however, would be magnificent for the fiendlord.
As for where I'd cut up the game for a trilogy, that's really tough. The firs fight against Magus is definitely one of the best ways to conclude that portion of the game: Marle has been saved, Frog's story has been explored, it's a very climactic part of the game, and sets you up for what will inevitably become the focus of the next two "films". But perhaps that'd be a bit much--everything from after 2300ad right before Zeal could also work as its own movie, leaving all of Zeal and its crazy massive climax for the final film.
This is kinda why I suggested a mini-series earlier; you could cut it up after every mini adventure has concluded. One episode for when you save Marle and the ensuing trial, one for when you find and fix Robo, one for when you defeat Magus for the first time, one for Ayla's cool stuff, one for Zeal, one for the finale, etc.