Here's my take, which I've been using for about a year and a half:
D&D XP chart (simpler, and I'm running modules written for D&D)
Races per D&D minus Halfling and Gnome, with the latter pair replaced by the Faen; there are also Litorians, Verrik and Sibecai in the world, but they're mostly far-off from where the campaign happens to be set, so they've made few "on-screen" appearances. The current party is three humans, three Faen and an elf.
Classes:
From D&D core: Barbarian, Bard (adapted to UA-ish spellcasting), Fighter, Rogue, Ranger and Monk (I hate the Oafsworn)
From AE: Champion, Magister, Mage Blade, Witch and Runethane
Other: A so-called "Sorcerer" which is the Shugenja in all but name has been a very important class. There is also a Swashbuckler which is not much like either the D&D or AE (Unfettered) version, and a Shaman which is about 70% the same as the Greenbond. I would allow the Scout from CA, the Knight from PH2, and the Warlock from the other CA with no issues, and the Ritual Warrior and Totem Warrior have been mentioned (and the Totem Warrior has even been seen "on-screen") as base classes that are specific to certain cultures.
I allowed the psionic classes at first (and zapped most of the psionic spells), but now regret this and wouldn't do it again. If I had it to do over, I would also just AE-ize the Druid as I did the Bard, rather than try to adapt the Greenbond. The Monk needs a rethink because some of the Feats I allow, the Monk's built-in AC bonus and the fact that I use a class-based Defense bonus combine to allow some pretty broken stuff to happen there. Other than that, I'm happy with the choices I made.
Magic System: Uses AE preparation-and-slot system and charts, with somewhat more limited weaving (the Bard uses the Mage Blade charts). Uses Wizard-like spell learning - you know as many spells as you can prepare, plus a few extra low-level ones, automatically, and can learn more by acquiring scrolls, spending some time and money (usually less than in D&D), and making a Spellcraft check. The exception is the Sorcerer, who automatically knows exactly as many spells as he/she can prepare and has no way short of burning Feats to learn more. Uses the division of spells into Simple, Complex and Exotic for all classes except Sorcerer, which has its own seperate chart organized by element (it's somewhat like the difference between Arcane and Divine magic in D&D). All classes, even the Sorc, use the AE system of Heightened and Diminished spells.
Complex spells are NOT learned by level, instead Complex and Exotic spells are divided into the five colours of Magic: The Gathering, and Feats allow you to learn spells of a particular colour and ANY level. This makes high-level Complex spells easier to learn, Exotic spells a little harder (you need access to the colour and THEN to spend a Feat), but also forces casters to keep their spells at least somewhat thematically similar.
Many spells listed as Exotic in AE are "demoted" to Complex or even Simple, but tend not to be available to Sorcerers. Many spells from Rokugan products added, which tend to be easily learned by Sorcerers but Complex, Exotic or entirely unavailable to the other caster classes.
Feats: More generous than either AE or D&D. Uses the concept of Talents, but not of Ceremonial Feats (actually, a few Feats are effectively ceremonial, but these are rare enough that it's just written into their descriptions). In general, most feats from either setting are available, and I am in the process of converting selected Masteries and class abilities from Iron Heroes over as well. (The main exception is the Feats that grant spell templates, and again, excluding them is now something I regret and would undo if I had it to do over again).
Skills: Almost entirely D&D 3.5, with three added skills from other d20 sources. Of all the skill-related things AE does differently to 3.5, the AE versions of Tumble and Concentration are the only ones I use. (Hide and Move Silently remain seperate, Knowledge skills are split as in D&D, there is a Profession skill, the 3.0-specific skills like Inuendo remain gone, etc). Challenges and such as per Iron Heroes are slowly being introduced. All classes are given at least 3 skill points per level, class skills for some classes are slightly expanded, and there are relatively easy ways to get an additional class skill or two.
Other: Action Points are used. (I don't use IH tokens. Things from IH that involve tokens sometimes cost Action Points instead, with an Action Point typically being worth around five tokens depending on the ability). A system for death and dying which is more generous than even the AE one is used, which I beleive I've discussed elsewhere. Paragon classes for all races are available. It is very hard to get access to evolved levels short of (sometimes literally) selling your soul, but they exist.
