I can't help but think Runes are going to do more than just add to your spiffy Skills. I can't help but wonder if runes will come with 1-2 Prefixes like a Jewel. Or perhaps the higher level runes will have 2-3 or so on.
So take example early on you find a minor power rune with 1 prefix, 10% damage done to undead.
I don't think anything major should be included into runes like 100 health or 10% FCR but maybe depending on the rune there is a prefix that could go with it.