The first thing I'm going to tackle is the role of magic (and psionics) in the world. I plan on using arcane and divine magic, psionics with the "psionics are different" rule, and incarnum. But I'm not really happy with the current way that arcane and divine magic are under the standard D&D rules. I feel like there should be more of a gap between the two. This is where I need some ideas.
I'll give you what I've got so far...
Arcane Magic: Dragons will be one of the oldest creatures in existance. Arcane magic may be descended from them in some way. I might use something like the creation of Eberron for this one, with some "progenitor" dragons, who will be very powerful entities, though probably not gods. Arcane magic is everywhere in the world, free energy waiting to be harnessed. Wizards learn arcane formulas to manipulate this energy through somatic, verbal, and material components. Sorcerers will draw on the "dragon descended" or "dragon touched" theory. In this world, however, sorcerers have no need for material components for the most part. If I can somehow balance the material component cost for more powerful spells, I may get rid of those for them as well.
Divine Magic: Deities and outsiders will be some of the oldest creatures in existance as well. Divine magic comes from one of these sources. I'm kind of stuck as to whether I actually want "deities" in my game. I may just have very powerful outsiders "grant" spells through their philosophy. This gets rid of one of the things I dislike, which is the power conflict between outsider lords and deities (especially in the case of Asmodeus, and whether he could beat a god, yada yada). There will most likely be no "god" or any such thing of arcane magic, since that kind of mixes between the two, while I'm trying to separate them. I'm still kind of stuck on what to do here, so this is where I need ideas.
Psionics: While arcane magic is outside energy harnessed by the strong, and divine magic is outside energy bestowed upon the faithful, psionics are pure will of the mind. Thus, the "psionics are different" rule. It is not magic. It just is. Though, there may be ways that magic can interfere with psionics, just not in the dispel magic or SR sense. Some creatures always have psionics, such as aboleths and mind flayers. A psionic humanoid is more rare. Psionic individuals will be much more powerful in this setting, as there are few who are aware of psionics, and fewer still that have any capacity to defend against them.
Incarnum: Incarnum is the power of the soul. I don't have Magic of Incarnum yet (since it hasn't been released), so I'm not sure what, if any, changes I will make to the way it works from the way it is presented. I had one idea though. Since incarnum is power derived from souls, and a person's essentia is based on the power of their soul, I may have some sort of soul-bonding thingy. With this, fiends and individuals who know the proper rituals and such can absorb an individual's soul, destroying the dead person's identity and adding the its power to the power of their own soul. This would, in game mechanics, increase the person's essentia pool by some amount, and possibly have other effects (based on what else I learn about incarnum and such when the book comes out). I feel this gives more meaning to the "fiends want souls" thing.
That's all I have for now. I welcome any ideas on any of these subjects.