It had issues, sure.
1. You should have been able to edit rune pages in champion select.
2. The IP sink that was "unlocking every rune" was absurd.
3. Tier 1 and 2 runes were just a trap, flat out.
4. The differences in power between runes were astonishing.
...but none of those made the system irreparable.
Issue 1 was a simple fix.
Issues 2 and 3 **were fixed**, but you waited to do it *until Runes were set to be phased out*.
Issue 4 is a simple matter of balancing out runes, something I don't recall happening since the removal of Dodge Chance.
Sure it wasn't super interesting, but it didn't have to be.
Hell, I'd rather this kind of thing *wasn't* super interesting.
Power along the lines of Electrocute, Conqueror, Lethal Tempo, Predator... none of this shit should be a part of the runes, it should be in the form of new items, summoner spells, and champions.
It's not like it was devoid of strategy, it just *looked* that way because you didn't *let us* strategize by editing runes.
Stacking armor as Amumu top to become immune to minion damage? Sure.
Hybrid Pen Thresh for all in damage? Seems legit.
XP runes on Talon for first blood? Sounds good to me.
Masteries are the only one that needed a rework. For those, I think something along the lines of the Odyssey customization (at a lower power level) would have been the way to go.