I think I understood you - by "stepback" I mainly referred to "less choice usually isn't a good thing" an such.
But as they explained, there will be simple +stats runes in the minor runes still.
As I got it, they are trying to give more real choice and get rid off the mandatory ones. Like look at an adc runepage, it is 90% the very same except some mr or lifesteal here and there, based on the champ and personal preferences. Now they will merge the mandatory ones in champ stats and turn the real options into minor runes, so you still will be able to fine-tune your stats based on your ideas, I think.
Keystones runes - what you only can have one afaik - simple have the same roles as keystone masteries.
And major runes will have the role kind of the more important masteries now.
So they are trying to keep all the versatility and options and just clean up the useless mess around them.
And based on what they wrote and the picture in the article, I'm sure that you can save the new rune pages just like mastery pages now and you can even tune them in the pre-match lobby, just like now.
I don't say they can't mess it up terribly at the end, it is a good habit of Riot sadly. But the idea in it's current form is very promising I think, and I don't see any real "loss" in it.
But as you said: we will see.