I'm pretty sure the only way that the rune system will ever work "properly"
and not massively favor a minority subset of the champion pool, not be a balancing nightmare, and actually allow players to somehow express their own playstyles.
Will be if riot somehow converts all of the runes into numerical sidegrades instead of upgrades.
and even then, i'm not sure it would work right, because there are still mechanical advantages/limitations that make some champions overwhelmingly favor curtain runes.
Actually i just thought how silly/fun it would be to play 
and take a version of Lethal Tempo which exchanged damage per hit, for number of hits, and try to mass stack his passive for a huge gold payout by trying to constantly juggle 3-4 axes.