The Runestone system was originally created to add flexibility to character skills, and to give players a chance to experiment and play around with new abilities after they had gained them through leveling up. The original idea had ten different effects that could be added to various abilities, including striking, lethality, efficiency, life-stealing, poison, slowing and so on. But ten was too many, Blizzard decided, and they opted to boil them down into five different stone types (Crimson, Obsidian, Indigo, Golden and Alabaster) that would each affect skills in a few different ways.
Cheng said having actual stones in the inventory worked in a few different ways. It gave the system a sense of discovery, as players enjoyed seeing which stones granted certain effects, and it accomplished the original goal of allowing players to experiment with customization. Managing the stones in the game's inventory was a "nightmare," according to Cheng, and player expectations didn't always match what the stones actually provided.
In the end, the team went with the existing Skill Rune system, which allowed Blizzard to give specific skill and stone combinations more "flavorful names," and let the team make sure that the added effects were appropriate for the skills they matched. But Cheng said the effects were still in there: Some runes still slow opponents or add more damage to attacks, and those were the effects originally conferred by the stones of Indigo and Crimson.