It's not the juctioning system that's the problem really, it's that they made it incredibly easy to obtain powerful magic that made all of your characters into demi-gods. Not only that, offensive magic did a pathetic amount of damage if cast under normal conditions, leaving it pretty much useless in battle.

So really, the junctioning system was fine; it was the utterly moronic implementation of magic within the game that made the battle system a joke.