I think it's stupid that every level 60 char can now use every skill without farming any items.
I see that it's a problem having over 3000 Items as Runes, but I think you can solve this better.
I would keep the old runes, but as soon as you equip them, you "learned" the runestone forever. You can skill switch it out, but not back into your inventory. Your Runestone becomes a skill. So you still have to find it and you still can switch it out, but you dont have the inventory issue.
That's my idea. I already had this month ago, but as it seems ... blizzard doesnt like it :-(