I think part of the issue with this is that it is difficult for League to laser-focus its balance on specific champions. The moment an item or rune gets changed, dozens of champions end up having their own balance thrown off, because they either use that effect or are especially affected by it. Because items and runes have always received frequent changes, it's difficult to really fine-tune vast amounts of champions every two weeks, or even every four weeks, in response. In a stable game, whichever champions don't receive immediate attention should not necessarily have to be in need of attention, but as it stands League isn't really there, as it does feel like most champions are receiving either far too much or far too little attention at any given time.
I also feel a recurring issue has been that Riot still has difficulty finding their footing in League's balancing environment. Changes that are intended to be either power-neutral, or only slight pushes in one direction or the other, end up throwing the balance of the target champion completely out of whack, and even new designs sometimes generate critical failures in gameplay, forcing them to inevitably be overnerfed in view of an eventual rework. Part of this problem may simply be that League's balance environment is too complex to fully grasp at any given time, what with its layers upon layers of different interconnected systems, but I think part of the problem may also be that the environment itself, and its underlying ruleset, changes radically over very short time intervals.
Whereas MOBAs like Smite, Dota 2, HotS, etc. only rarely add new items or implement other systemic changes, League adds, removes and reworks items with much greater frequency, all while implementing similarly large changes to runes, Summoner's Rift, and sometimes summoner spells too. This, in turn, creates a different meta in which different mechanics are stronger or weaker than before, thereby changing the way one would have to gauge their power. It's this constant instability that I think is at least partially responsible for so little of League's roster being considered good at any given time, and while I appreciate that Riot has tried to shake things up, the long-term result is that a ton of resources have been wasted on whack-a-mole-balancing, when they could have gone into much more durable improvements, and stabler champion adjustments.