I prefer AE's magic system. First, the spells are not as obvious to choose. Which 3.5 wizard wouldn't choose to prepare fireball or lightning bolt? Magic Missile, Invisibility? While many spells of AE replicate standard spells, this usually makes them either more balanced, more adaptable, or both at the same time.
More balanced, as in Mud Ball (dmg 1d8+1/level, blinds target) compared to a Magic Missile spell. Or Raise the Dead (Cast seven times during seven days to bring subject back to life).
More adaptable, as in Energy Bolt (type of energy depends) compared to Lightning Bolt.
Speaking of adaptability, spell templates as well as rules to weave and laden spell slots makes the whole thing much more versatile without using stuff like Power Points, like say Psionics - I do not really like PP because it's like a double-system for supernatural abilities when used with standard spellcasters.
Which explains as well why I would not mix AE's magic system with the PHB's. It is possible to use them both though, some on this board did mix them. And I wouldn't be against the use of the sorcerer of BOEM in my AE campaign.