So something that's a little bit concerning about this new Rune/Mastery system
I feel like i've seen a similar change before http://imgur.com/a/iZMwH
and as many probably know, that change went over sooooo well...
If you want this kind of system to exist, then you're gonna need to design the game from the ground up with it in mind. But people have attempted to design these systems into their core game design and those games have generally failed to acquire a comparable audience on their own merits (D3).
I get where riot is coming from in their attempt to simplify the systems, but unfortunately a simplified system means a simplified appeal. The less broad a design, the less broad the appeal, the smaller the audience you will have.
They keep building up these systems on the back of the old design, which earned it's popularity, but have, and continue to, slowly phased out that design. The more you do this, the more people will decide that they didn't sign up to ride on this boat, because while you can share the same name and visual assets, if you change out every functional part of a ship, is it still the same boat? Does the identity exist as the whole or does it exist as the sum of the pieces?
Edit: Mind you, that's not to say that you should stagnate and let the game get boring. Only that you need to respect the old design, if you want to retain your audience.