Champions with high ap Ratios, like Chogath and Annie, benefit very well from the flat AP Runes. You could buy a Doran's for even more AP, and some basic starter stats in hp and regen/passive. Or , with flat AP Runes, buy an Armor Cloth if you're mid laner is ad, or lots of sustains tools to outfarm your laner from the first engage (runes providing the AP you would not have without buying the Doran's) However, if your champ has abilities with high base dmg, magic pen is more effecitve. High AP = Useful magic pen. Low AP = Magic Pen not so important. It's like having tons of atk speed without any ad to back it up. IMO. I can often get a fb as Annie or Liss (ratios not considered) with high AP Flat runes. People don't have mr early on (another reason to go flat ap over magic pen for early advantage) but if you can't snowball the enemy will pick up MR and then it's not a walk in the park.
Scepters. Btw.