It offers a % damage increase for all of your magic abilities, and a lot less champions gain magic resistance naturally, and unless they're directly countering you, they won't build it until after the mid-game, meaning a larger portion of time to dominate. AP runes, on the other hand, offer, at best, 1% damage increase at level 1 (per rune). The bonus they give is less effective the moment you buy AP items. As well, unlike AP, where each point of AP is not as strong (relatively) as the point before it (same with AD), Magic Penetration becomes stronger the more of it you have (up until the enemy is at an effective 0 Magic Resistance.) This means, with a pretty common mastery setup, and buying Doran's Ring at the start, you are already overshadowing the effectiveness of your AP runes. Yes, on certain champions like Vladimir (who has a heal based on his AP, not on his damage), more AP is better, but the differences for those particular champions are close enough that it's an either-or pick. For everyone else, Magic Penetration runes are better.