A little late, but I'm a big fan of
Fantasy Craft by Crafty Games. It's designed by the same folks who did Spycraft.
It's a d20 based (but you should forget 3.X and Pathfinder). Classes are different and well balanced from aa spotlight sharing perspective, but no one is worthless in any given arena. Species options out of the book include golems, drakes, giants, and ogres that are balanced with humans, elves, etc but still feel like golems, drakes, etc. The system for building species and specialties is fairly straight forward.
Arcane magic, divine magic, and magic items (consumable and permanent) are completely all different systems and both are completely and independently optional. NPCs and DCs scale with the PCs by default so while the PCs get more tricks every level, their numerical advantage grows much more slowly. With the right Campaign Qualities it can be very gritty. The system's very robust and hard to break once you understand it's philosophy. You can build a PC which will be unbeatable in one of the minigames, but you'll suck in the others. Heavy specialization is as much a way of telling the GM how you want to fail as how you want to succeed. Combat involves class based BAB, Initiative, Saves, and Defense with Armor as DR but skills (including social skills) play an important role in combat as well.
There are three classes specialized for out of combat activities (the Courtier, Keeper, and Emisary - social monster, Expert on steroids, and spy/agent/detective respectively) but their not worthless in combat. Similarly, even a Soldier, Martial Artist, or Lancer (combat master, different sort of combat master, and knight) have the ability to hold their own in social or other encounters. A Soldier will never out social a Courtier or vice versa. Similarly, a Mage will never out anything any other class (other then casting spells, obviously) but they can equal them or do pretty good at all of their jobs.
To give you a sense of the flexibility, the game has four settings given write ups in the books. Sunchaser is a high fantasy setting with some fairy tale influence, high concept is Lord of the Rings on the Mississippi. The Realm is a bare bones setting that is darker and grittier then Sunchaser, with the forces of the Church in conflict with the Circle of Mages. Neither are the heroes, and there's a Frankenstein, mad scientist/mage feel. Cloak and Dagger is set in a Romanesque Empire that's seen it's best days. Epoch is straight up swords and sorcery, with twist of drawing from North America. Think Apache versus invading (demon worshiping) Aztecs.