My thoughts exactly. When Runes Reforged was announced to us, I made a thread that said much of the above, explaining that the system would ultimately do nothing to fix the mistakes of previous mastery systems. Once the dust settled, we'd go back to having a solved game with little added gameplay or diversity for anyone, and the game would be just as difficult to balance as before, if not more difficult. I was not the only person to suggest this, either. Fast-forward to now, and to no-one's surprise, that's exactly what happened. One did not need several years' worth of game design experience to realize that repeating the exact same structural mistakes as before would lead to identical structural problems, though that certainly did not stop Riot from following through with an update that created huge disruptions in balance, for little to no positive long-term impact.
At this point, I think Riot needs to realize that any kind of generalized bonus system, no matter how refined or overly strong, will simply not be good for League. Any such system will fail to generate meaningful diversity, and will only continue to generate balance issues and design limitations, as champions will be forced to remain functional under those bonuses, often to the point of being balanced so hard around them that they become dysfunctional otherwise. This is why I think Runes Reforged needs to go completely, and beyond that Riot should also reevaluate what they want out of summoner spells and even items, both of which are systems I think have also aged poorly. Summoner Spells were once a selling point that distinguished League from the competition, along with its runes and masteries, but in the long run the system has ended up homogenizing the strengths and playstyles of many champions, as well as warping the game's balance in unsavory ways. Similarly, items were once intended to allow players to fully customize their champions' playstyles, but that fell apart very quickly when Riot realized that certain stats and effects were simply not healthy on certain kits. At this point, none of these systems generate real diversity, and frequently they fail to generate meaningful gameplay as well, with marksman items in particular still mostly acting as stat sticks. Additionally, all of these systems only complicate balance further, adding layers upon layers of conditionals that hamper the devs' ability to focus on what makes certain champions specifically imbalanced or unhealthy.
At this point, we have plenty of MOBAs that have shown greater diversity of gameplay, as well as stabler balancing overall, via entirely new customization systems that are tailored to individual champions, such as HotS's talent system. While League should probably not try to copy these systems, as Dota did, Riot could certainly take a page out of those games and try to streamline its own systems. Both summoner spells and runes can be rolled into itemization, particularly since there's a ton of overlap between these systems (e.g. Second Wind and Spectre's Cowl, Overheal and Bloodthirster, Cleanse and QSS, etc.), and doing so could even help Riot achieve their other goal of trimming down lobby durations, which currently they've attempted to pare down by limiting actual strategic depth for players, i.e. by having everyone ban a champion all at once instead of going through proper pick/ban phases.