My only real issue with Runes: Reforged
So way back when Riot announced that they were reworking Runes, they said they would be compensating champions with Base Stat buffs.
Naturally, and especially as a Jungle main, I was quite apprehensive. Pretty much every Jungler that I play had some level of dependency on super-specific Rune Pages. Elise needed Attack Speed Marks. I ran scaling HP seals on all of my Tank Junglers. There were a few slightly gimped Tank junglers that needed Armor Seals and Quints. The list goes on and on.
Fast-forward to the 7.21 (PBE was on 7.22) and my scepticism turned out to be valid. It turned out that Riot had made very blanketed base stat buffs. They did little-to-no research into the champions they were changing. Elise didn't get any base AS. Gragas didn't get any Health or AP. And none of my tank junglers apart from Nunu got any HP or HP growth changes.
Runes reforged really hurt a lot of junglers.

even stronger than focused kits because of the flat 'balance' you're talking about...I don't think it has anything to do with the jungle role but more with the non-reasearch you are talking about which really seems like typical Ghostcrawler-led Riot.