I strongly disagree with a lot of this post.
I mean, I actually agree with the overall idea - you need to recognize the problem directly when nerfing someone, you can't focus on the irrelevant part and hope that making something else weaker will make the problem disappear.
Just that I disagree with the examples.
Ryze: His mana scaling could disappear, but how exactly is mana scaling a huge problem? There are plenty of champions that seem to not have a problem when they scale offensively with armor, health, MR, etc... so why should mana be any different? His root CAN'T disappear. It's too strong right now, his burst pattern is too strong, I agree. Ryze is a sustained damage dealer who can burst a squishy in one combo just like any assassin, THAT'S his problem. An unfed Ryze can root the ADC and 100-0 them while keeping them rooted the whole time = an assassin. However he can also deal good rotations on damage on low cooldown = a sustained damage mage. Sustained damage + assassin burst is NOT balanceable, ESPECIALLY on someone who is tanky too! Don't get rid of the point-and-click root though. There's so much mobility in this game (e.g. Ekko and Kalista that you also mentioned) that having targeted hard CC is really important. There need to be these ways to deal with it. Ryze shouldn't be able to combo multiple roots together though, the combo should be that he roots someone and an ally can land their skillshot CC on the rooted enemy. Perhaps Ryze can combo his root a second time after the allied CC, I'd say that is balanced (and would make him still good in lane since any jungler with CC will allow him to get off 2 roots).
Ezreal: I don't think his on-hit Q is his problem. Sure, it breaks him with certain items, but Ezreal's problem is his safety. He has a flash in his kit on a fraction of the cooldown, on top of a global ultimate that lets him pick kills or just farm a big wave that's going to crash in to a tower. If Ezreal didn't have his blink, he could be balanced around stuff like Runeglaive. Make him like most other ADCs (i.e. longer cooldown and less effective dashing ability) and he'd be in a better spot.
Alistar: His W-Q combo is perfectly fine. There are a plethora of other champions that can do largely the same. It's a 1 second knockup from 650 range. Compare to say, Maokai, who has a targeted 2 second snare from 525 range and can follow up with a knockback. Or pre-rework Taric had a targeted stun that no one seemed to have a problem with (I mean, he was strong and not popular). There's nothing wrong with targeted CC, it's necessary to keep the mobility in this game in check. When the competitive players are all playing super playmaking hyper-mobile champions, targeted CC is going to show up.
Braum: His shield is way less oppressive than Yasuo's windwall. Enough said.
Janna: Her ultimate isn't the problem with her at all. It's the fact that her power is so hidden. Her ultimate is the only part of her kit that actually shows her power at all. The problem with Janna is that even when she's the strongest support out there by a mile, no one outside of the LCS thinks she's insanely strong and banworthy. No one thinks they lost lane or game because Janna was OP outside of challenger. She suffers from everything Riot had commented on Sona about with the auras and stuff. If she's not super strong, no one will play her because her power isn't evident at all and they feel useless. So she has to be strong enough to carry a hefty win rate to convince people to play her. Keep the tornado and shield and ultimate, get rid of Zephyr and give her something that is more of a playmaking ability and she can suddenly be balanced and have VISIBLE power.
Gragas: His ultimate is unique and pretty good as well. Only problem I think there is with it, is that it should show a really clear indicator of where it's going to land for the enemy team. It would probably completely ruin him for competitive (as they'd all have good enough reflexes to flash to the side of it they wanted) but it only seems fair. As a side note, I think Thresh and Blitzcrank hooks should show some sort of immediate indicator as well, it's pretty silly that they can be facing one direction and then immediately cast in a different direction. A champion should not be able to start a skillshot and shoot it in a different direction. Same idea with Xerath and Varus, if you want to let them aim while they charge it fine, but then make the character turn towards where they're aiming.
Ekko: His problem was the compensation. He needed a net nerf, but got a net buff. The most successful tanky top Ekko build still has an abyssal scepter, which gives him enough AP that he doesn't suffer from the base damage reduction because of the scaling buffs. Add in runes and masteries, Ekko wasn't actually nerfed at all. Mid Ekko was just buffed. When I saw the changes I thought they'd do very little if anything. I agree that his kit is outright broken overloaded, but that doesn't mean it can't be balanced without a rework. Tank Ekko should do basically 0 damage. He was made to be a new type of assassin that had better utility and less damage. That's cool and fine, but since it's unique he should be pigeonholed in to that role. The base damage increases on all of his abilities should be greatly reduced (e.g. 40/65/90/115/140 to 40/50/60/70/80) and then give him AP compensation so that it evens out his damage combo at level 9 when he's around the average AP you'd have at level 9, 13 at 13, 16 at 16, and 18 at 18. So e.g. at 100AP / 200AP / 300AP / 400AP.
Kalista: They've actually changed her passive a lot. The problem though? The slow removal of all point-and-click CC. The best solution if they want to continue going this way? Make her more like Kog'maw (i.e. she has to stand still to deal even close to optimal damage), her jumps should drastically slow her attack speed. So sure, she'd still be just as hard to hit with skillshots or chase with a tank, but she also can't do nearly as much damage to you in the process. If she's fighting the enemy ADC in mid-late game she needs to stand still or she'll be simply outdamaged. So in a teamfight she does way less damage than the enemy adc since she has so much safety. I think it would also help clarity a lot if they put an indicator on how much damage her rend stacks would do to you. Too many ADCs just die to Kalista in lane because they feel like they can survive her rend and they can't. E.g. They had heal and didn't think they needed it and she gets rend off right before they kill her and they die. E.g. They could have ran away earlier and underestimated her damage. Her rend stacking mechanism hides a lot of her power - pro players rending too early on Baron really show that even people who play a lot of kalista don't have a good idea of how much damage it will do. Make it clear to people how much damage she has stacked is a good step towards making her balanced.
Unique champion traits can be annoying, but they also bring more diversity to the game. Some people like this. As long as it's balanced appropriately, it should be fine. I think a lot of this stuff can be balanced as well - it just takes more work than normal.