Junction system is my favorite skill system in the series, hands down. Drawing? Maybe not, but I actually didn't mind it much. They were attempting to create a system where time and effort was rewarded with better stats and magic. Where they failed is to make that process enjoyable. For me it was neutral, for others it was bad.
However, over the years, I've racked my brain for alternatives, but I have never thought up any way of gaining magic (as items) that would be dynamic enough to work. Finding magic in chests/draw points just makes it like any other item. Monsters randomly dropping magic at the end of battle, once again, makes it far too static and linear. Drawing within battle just adds a dimension that is really different from any other RPG. It's sort of like grinding, but without doing lots of individual fights. The only other game that rewards staying in battle longer than simply defeating enemies, that I can think of, is Ar Tonelico. In any case, while the drawing part may be a critical flaw, I applaud S-E for trying something so against-the-norm that it practically rewrites the foundation of the RPG system. The idea of Magic as a finite item is an interesting and unexplored one. And I think they just about got it, with some unfortunate flaws.
But someone mentioned transition length and battle speed. This I agree with. Had they been able to completely streamline all the repetitive aspects of the game, it would have been FAR less obnoxious to fight and draw. GF animations were ridiculous and un-skipable, scene dissolves and wipes were ungodly long, battle animations couldn't overlap (this one would have saved a lot of time), and everything is just a bit sluggish. Not that FF9 is much better (though transitions were much sped up) but you had not incentive to fight over and over again. Honestly, this would have been the easiest thing to fix and I believe would have made the game much more appealing.
It's still my favorite RPG, but I understand it's flaws.