I'm not including gnomes simply out of a sense of completeness; I've dropped half-elves and half-orcs, and added 4 additional races (including half-goblins), so I'd not be worried about dropping more PHB races, if I can't think of how to use them well. But I like gnomes, and I want to keep them if I can. I think I'm coming up with something at the moment that might make them rather special.

In terms of making religion ambiguous, the only thing that can really be taken as proof of the existence of gods is the existence of clerics. And plenty of people argue that bards and druids can do pretty much everything clerics do without assuming the existance of divine beings. Mostly clerics just do the theological equivilent of putting their fingers in their ears and singing "lalala I can't hear you".

As for alignments, they're mostly easy to drop; No alignment domains, no spells that have specific alignment effects (protection from chaos, magic circle against law, detect evil, etc). The dificult bit came with paladins. At first, I thought of only having certain deities (those that would traditionally be considered "good") sponsoring paladins, but in the end, I figured that was a step backwards.

In the end, I decided that a paladin was simply a holy warrior, fighting for the ideals of their religion, and that there was no reason why every god shouldn't be able to have paladins. They can still detect and smite evil, but the definition of "evil" varies depending on the dogma of the specific deity. Lay on hands can either cure or inflict, depending on whether or not clerics of that deity can swap out for cure or inflict spells, and they can turn or rebuke undead, again depending on what clerics of that faith can do. It's suprising that even with those small changes, a paladin of a god of thieves and assassins is very different from a paladin of a god of borders and boundaries, whose main goal is stopping the dead from being raised.

[Continued...]

Also, I'm getting rid of Holy Avengers, in favour of making a unique holy weapon for each faith. in the case of the two gods listed above:

Shadowblade
In the hands of anyone but a paladin of Flay, this plain, black iron blade functions as a simple +2 dagger. If the wielder is not a follower of Flay, the blade is treacherous, twisting away from the vital organs of its target; in such hands it is treated as having an enhancement penalty of -2 when rolling to confirm a critical hit. In the hands of a paladin of Flay, the shadowblade gains several additional abilities; it becomes as a +5 dagger that deals an additional 3d6 damage when the target is denied his Dexterity bonus to AC. This stacks with a rogue's sneak attack ability. A paladin of flay can also command the shadowblade to change into an unadorned black ring (or back to a dagger) on his right middle finger. While in ring form, the shadowblade appears non-magical to any detection less powerful than wish or miracle, but still counts towards the number of magical rings the wielder can wear. Finally, when drawn (and not in ring form) it can wrap shadows around its wielder, granting a +10 competence bonus to Hide checks.

Hammer of Charos
This maul +3 has a steel haft and a wooden head with copper caps decorated with skulls. Upon command, the Hammer of Charos is sheathed in fire. The fire does not harm the wielder. The effect remains until another command is given. It deals an extra 1d6 points of fire damage on a successful hit. It acts as a +5 weapon against undead, and deals an additional 2d6 damage against them. Any undead stuck by this weapon must make a Will save (DC 14) or be destroyed. It deals damage normally against incorporeal creatures; An incorporeal creature's 50% chance to avoid damage does not apply to attacks with a Hammer of Charos. When undead are within 100 feet of the hammer, the caps turn a deep black as they emit a powerful negative energy effect; any undead within this range must make a Will saving throw (DC 18) or move towards the wielder. Non-intelligent undead move at their standard move rate; intelligent undead may move faster if they so choose. They must move directly towards the wielder, and cannot attack any other target, unless they are attacked first.