First off, subjectivity plays a large role in all these things.
Items in game are balanced for a healthy metagame, not based on math. For example, Riot felt that survivability was too cheap/accessible/overpowering, so they gave survivability items a 10% nerf in effectiveness across the board (in addition to heavier nerfs to Catalyst and others). Giant's Belt for example is way less effective than its original implementation (which was fricking godly, lol. It was 500 HP for 1000g, or 2g per hp. Then it was 500 HP for 1100 gold, then 450 HP for 1100 gold, then 450 HP for 1150 gold, then 430 (or is it less now?) HP for 1150 gold). These aren't based on comparing a math equation to crit chance, but just how they want the metagame to evolve.
Runes were implemented a LONG time ago, and rather badly at that. There have been a couple revamps to specific runes, but it's still a case of balancing for the metagame rather than easy math equations by this point. When the Store came out, instead of rebalancing all the runes to make them as equal as possible in strength, they fixed the edge cases (HP quints way OP, MPen runes way UP) and just priced on popularity.
Again, I don't really mind. It's kind of the same thing with Champions: some people are outraged that they price them differently (regardless of whether they are tied to champion strength or not). I just think it's good business. Most all of the runes I buy are the most expensive ones, because they are my favorite. Doesn't really bother me, because I still don't feel the prices are excessive. I play a bit more than the average casual player but far, far less than a hardcore player (when I played 18 hours a day sometimes back in beta :P).
Pricing is just so subjective.
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