It is still very confusing for newer players to work up a good rune page, in my opinion. They shouldn't have to look up a guide to have useful runes and so their decision should actually matters. No way a new player would know how to build a Rune page from scatch, and if we would make all the runes for free, it would be just chaos. I like the idea that they made Tier 3 standard runes 50% though. But then again there were a lot of bad runes which were useless. Most of my rune pages were also adapted to a certain champion and not more which forced me to have a certain champion pool or force me to buy more rune pages.
You can nicely change your runes in champ select with the new system and if you had that on the last rune system it would be cause. You could literally just buy up a lot of runes and then wait for enemy pick and making a rune page that would totally ruin them.
Edit: The amount of useless rune pages I've seen in my life.. even in higher ranks.