What if players started out with a basic rune set?
With enough runes to fill out the player's rune page, but only containing the most basic/universal runes? (eg damage marks, health seals, ap glyphs, and health quints or some other standard layout)
As crazy of an idea as this might be, it would at least mitigate raw stat imbalances between lvl 30 and pre-30 accounts and smooth out pre-30 jungling issues while still leaving enough incentive to sink ip into the wide variety of other runes for customization (AS, Lifesteal, Armor/MR, Movespeed, Attack Speed, CDR, etc.)