If you are religiously sensitive, this thread may offend you. I'm not particularly religious so anything that's out of place- please let me know.
I was looking at all the divine classes and I realized that they kinda ignore the religious elephant in the room in general. In some fashion, a lot of the divine abilities and spells are linked to the Abrahamic religions. In particular, the miracle of Jesus and his disciples/ the saints/ the clergy. (The Paladin's mercies read like the Wikipedia article on the Miracles of Jesus :D)
As a high level prestige class, how cool would it be to start gaining some small sliver of divinity? (Like entry set to somewhere around 15th level) It would be a class that would grant divine spell-like abilities a number of times per day (probably based on Charisma). Maybe treat them like "divinity talents" so you can pick and chose when you get them.
Stuff like:
Cure
-Blind
-Disease (Magic or Natural)
-Paralytic
-Bleeding
-Deaf/Mute
Exorcisms
-Allow others to Exorcize people in his name (like the later level Paladin ability to grant others Smite)
Resurrect
-Himself
-Other (Word of resurrection?)
Prestidigitation
Create food and water
Control weather
Wither/Grow Crops
Either that or have it be a starting trait/"race" (to negate the racial bonuses in place of this) that represents a "touch of divinity about you". Hell, that makes me think of giving a unique Sorcerer bloodline/alternate class with divine spells/abilities.
Any thoughts about becoming a Messiah? (Obviously, it would be some kinda in-campaign thing.)
The Godling book has something much like this, the child of a "god" and all, but it's a core class.
For PrC, I would suggest looking for the Paths of Faith book by Fantasy Flight games, and amazing book as far as anything divine would be needed for the game IMHO.
FYI the term Messiah means "The promised deliverer of the Jewish nation prophesied in the Hebrew Bible". So it would then mean in turn that the Abrahamic "god" would have to exist in your world then for the use of that term.
Have you looked over Green Ronin's "Testament" campaign setting?
It's based around playing a biblical game, and has many spells, feats, and classes that are unique to that setting. It may have something to offer you.
Play an oracle with the right mystery.