I ran an AE/3.5 Hybrid game for 5+ years from 1st-23rd level.
All classes were allowed and my general rule of thumb for scrolls and wands and the like was if there was a spell that had similar effect....in AE and 3.5 then both casters of each magic type could use it. Thus as a DM I did not have to supply wands of Identify and wands of Analyze.
I allowed every class to get access to the bonus true name ceremony feat.
I allowed multi classing between the 2 systems, and it worked fine (Fighter/Champion, Unfettered/Paladin/Knight of the Pale, Archer Totem Warrior/Order of the Bow).
I used a modified version of 3.5 skills, (much closer to
4e skill set) with Stealth, Perception, Arcana etc....simply made it if one feeder skill was on the list then the class got the combined skill. People were more effective skill wise, but that was what I was going for.
I eliminated Favored Class and allowed open Multi-classing.
As for class balance....the classes as a whole hold up pretty well.
A Magister, certainly pre Spell Treasury was a little more subtle than a standard Wizard lacking Magic Missle or Scorching Burst.....but with some planing could be the best buffer/healer in the game.
Dragon Mage can give some tremendous boosts to AC, and at higher levels Magisters can heal.
At points I had a Magister, Wizard, Druid, Warlock and Warmage, and honestly each class came out with a different flavor, and effectiveness in certain circumstances, but overall were pretty balanced with each other.
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