I don't recall if Keith Baker reads/posts here, but I'd love to get his take. (I can't seem to post on the WotC forums for some reason, so I was unable to ask on their Eberron-specific board that I know he haunts.)
My apologies for the delayed response - I haven't been on ENWorld for a bit.
My initial thought is to equate "runes" with the various dragonmarks scattered throughout the world, but I thought I'd ask in case there are better ideas out there.
This seems logical to me. However, to clarify, it's not specifically
dragonmarks that I'd use... it's
Prophecy marks, the symbols that appear on the world. Quoting
Dragons of Eberron:
In the past, the symbols that appeared on the earth were called dragonmarks. These days, they are usually called Prophecy marks. The design of these marks is quite similar to those found on flesh, but every mark is different; each line has meaning to one who knows how to read them. If a character who speaks Draconic makes a DC 30 Spellcraft check, she gains a hint about the meaning of a mark, to a maximum of five words. For example, she might recognize the concepts of “king,” “victory,” and “moving stone.” Although interesting, this hint rarely provides full meaning, and might actually be misleading.
A small Prophecy mark might be the size of a human fist. The largest marks are so big that they can be seen properly only from a great height. All marks radiate a strong aura of universal magic and occasionally shimmer with a blue-green radiance similar to the color of dragonmarks. Prophecy marks slowly repair themselves if damaged. It’s possible to remove a small mark whole, but if a mark is simply damaged, it eventually re-forms.
Essentially, this precisely fills the concept of the runes in 4E - an all-but-forgotten "divine alphabet", whose symbols have power for those who understand them. A key point here is that a Runepriest does NOT necessarily have to be a student of the Prophecy itself; he could easily just be a student of the symbols of the Prophecy, understanding how this is the fundamental language of reality and learning how to tap its power as opposed to the big picture of what the particular inscriptions are saying. There's nothing wrong with a runepriest pursuing the Prophecy, I'm just saying that he doesn't HAVE to.
With that said, the first 4E Eberron character
I played was a cleric of the Prophecy itself. The idea was that he recognized that the PC group were people touched by the Prophecy with a vital role to play. He wasn't a scholar and wasn't a
student of the Prophecy; he pursued it based on faith, confident that the path would unfold. His divine powers were based around that - healing word as "It's not your time to fall!". He went Divine Oracle as soon as possible, and specialized in divination rituals, again with the idea that he had an intuitive connection to the Prophecy. Were I to make that character now, I'd probably make him as a Runepriest.
If I was running the character in my game, I'd ask the PC what rune feats and powers he hoped to get in the future and base some of the adventures around actually finding the Prophecy Marks tied to those... essentially saying that to gain some of his powers, he needs to learn more of the alphabet. In doing this, he could clash with agents of the Lords of Dust or the Chamber... or either force could seek to use him.