Well I've always thought this, but today I was playing malphite (whom I actually did very good as) and I wanted to tank of course. But I noticed that it was hard finding a team that armor would be good against. Sure I wasn't last pick but still, there first 2 and 3 champions usually had a good amount of AP and magic damage.
33 or so of the current 57 champions either have magic as their main source of damage (pretty much go AP every game), have other builds but go AP most of the time, or can go AP as opposed to a DPS build.
So thats about 33 to 24, not perfectly balanced but not that bad. But the problem is, even some of the dps and damage oriented champions do their fair share of magic damage through their abilities. The only champions that armor is a hard counter to are auto attack champions, which seem to be a dieing breed, there amount of heavy magic dealers and AP champions far out number the auto attack champions.
Now this isn't too much of a problem, I get tons of Magic resistance when I am trying to tank, but champions like rammus and Malphite were kind of built around armor, magic resist won't benefit them as much.
Its not really a big issue, only some champions are somewhat affected by it, but still, I'd like to see more spells that do damage instead of magic from ability power.