Looks good 2 me. For marks, magic pen is pretty standard for caster types and you are right that she deals mostly magical damage, (rageblade aside).
Yellow, MP regen is pretty valuable since she is a mana hog. Even then you will still want a few Doran's or blue buff or other mana supply.
Blue flat CDR is what I use for ALL champions. In theory one might occasionally prefer magic resistance or something, but nobody really has the rune pages for all that. Most people have a Caster setup, an AD setup with armor pen, and a jungle setup with AS/Apen and Armor on their yellow.
Ive got 1 additional for Trynd only and if I had more, Id consider a blue magic resist page for certain champs.