I'm currently eliminating the wizard class, and only allowing sorcerers and clerics in my campaign. The spellcraft skill and detect magic spell have been removed, instead using either knowledge arcana, or knowledge religion to understand items and their magical properties. I've also eliminated tongues and comprehend languages, since that almost totally eliminates the power and mystery of having different languages.
Magic items IMC are based more on physical aspects of objects. Thus, troll's blood is the stuff of magical curing potions, and the hide of a displacer beast can be suitably made into a displacer cloak. Magical items demand more from a skilled master crafter than from a wizard. In addition, magic swords and armors gain their bonuses from craftsmanship or from properties of the metals themselves, not from a magical spell. That makes dwarves the supreme smiths of the land, and elves the crafters of all things from exotic woods--and there won't be any learned wizards or clerics who would dare say otherwise.
Some other changes I've thought over, but am not currently using:
Making magic items a focus device for casting spells. So, for instance, a scepter with a special crystal on the end might allow it's weilder to cast all spells related to light at up to 4th-level of ability. This would include heightened spells, or otherwise metamagiced versions of light spells. I would probably limit an item's powers by giving them charges, and requiring some special way to recharge the item.
Making the maximum spell level able to be cast equal to the casters ability modifier. Now, an 18 WIS only allows a cleric to cast 5th-level spells. It may encourage casters to take one or two additional age categories in their race in order to gain better ability bonuses for their class. Finally, meeting an old wizard means you should respect their abilities!
Anyway, there are some of the things I've thought about.
