I ran an Oblivion game not too long ago. I treated it very Gestalt. I made custom races and improved the baddies to gestalt level.

I balanced this by forcing players to give me a concept of their character and i gave them a few class ideas early. It wasn't too hard.

Table topping with fatigue is pretty hard... especially since its a video game system and you don't wanna run a 4e. 4e has fatigue kinda set up by what power your going to use.

If you want the custom races we made... we integrated most of them into 3.5 races. Most of them should be +1 level adjust..without that adjust.

Additionally, we tried to stay true to the game as much as possible...so we included the stat out of powers (like eye of night) etc.

if you want em, send me a PM

-wrath