I'm just wondering what people think about this:

For a caster like anivia, karthus, kassadin, annie, CM, ryze, which runeset would generally yield the highest damage?

The choice is between 20 magic pen at lvl 1, vs 75 AP at lvl 18.

With the buffed boots, and the new guise, 40 magic pen is easy to get, which negates a chalice.

AP on the otherhand is probably better lategame, but i dunno.

Thoughts?

Maybe you are right - except for marks, magic pen is a clear winner here.

I bought AP in seals, quints and glyphs and magic pen in marks. So far so good.

The best would be a combination of both. Since magic pen is primary in marks and ap on glyphs.

You dont need magic pen boots. Mercury treads ftw. Neither do you need Guise. Not enough item slots to get mid tier items when you want to maximize your damage. I use 9th talent + runes + abyssal (for negative MR on people with less than 50 MR). I dont get guise or void or magic pen boots.

Thats exactly what I mean. You dont have many options on marks and Magic Pen is now primary on marks so it is still better to go Magic Pen on marks and AP on glyphs that AP on both... Simply because you will get something like 10AP or less from the marks. And by doing this you can skip on the magic pen boots and get the mercury treads which are way better (40 magic resist vs 20 magic pen not mentioning the OMG reduce stuns by 40%).