The quality of a champion is not purely defined by how good they feel to play, and that's why I think the OP completely misses the point of why many players dislike CertainlyT's champions. I absolutely agree that his champions tend to feel extremely fun to play, and CertainlyT is practically unmatched when it comes to giving a champion a flow and power that is completely unique to them. One of the greatest aspects of his champion is the agency they have: when mastered, they have so many options available to them that they kind of transcend the game itself with the freedom they have.
Trouble is, that agency usually comes at a tremendous cost in the agency of other players, both on the enemy team and even with the champion's allies: Kalista, for example, has this phenomenal kiting power and command over her partner, but the flipside to that is that some champions, namely low-mobility melee champions, have practically no way of dealing with her, and her activating her Black Spear and ult both yank control away from her ally, which can feel awful if both players aren't in sync with each other. On a more subtle level, Thresh sometimes feels unfair because he gets to do practically anything one could ask for of a support (he can initiate, save allies, poke, trade, tank and lay down crowd control -- all decently well), at a time when avoidance of hyper-versatility is extolled as a reason to either design champions with notable (and valuable) deficits, or tone down the kits of existing champions until they feel unsatisfying.
This is definitely not a problem exclusive to CertainlyT's designs either: Ekko and Azir, who were listed in the OP as well, are both notable for having existed in states where, at least past a certain mastery threshold, they have no substantial weaknesses. Azir is slated for a rework precisely because, even though he's terrible below a very high skill threshold, past that mark he can give himself far too much safety against even his toughest counters. The problem is that these champions, and more generally many recent tropes in champion design (e.g. complex, versatile kits, mechanics that appear to bend or break common in-game rules), feel like the result of a trend that originated with his champions. Suddenly, it's okay for a squishy champion to be able to nullify ultimate abilities, because that precedent has been set with Yasuo, and it's acceptable for a ranged champion to have more mobility than most melee champions because Kalista did it first. These effects aren't necessarily bad, but they are certainly polarizing, and when handled improperly can create really frustrating situations where a champion feels like their enjoyment and power comes at a cost in everyone else's.
Technically, you could have an environment where everyone would have as much personal agency as Yasuo, Kalista or Thresh, but a risk of that would be creating a game in which personal enjoyment could end up turning cannibalistic, with everyone treading over each other to feed their own fantasy of somehow superseding the game's conventions and feeling special as a result. On top of that, CertainlyT's most infamous champions also happen to be particularly tough to use properly: sure, they have a ton of options and a great flow, but until you understand all of that champion's intricacies and how to piece their complex kit together, you're not that likely to succeed. By contrast, a great deal many champions have achieved similar depth, if not greater depth sometimes, with far simpler kits, all while properly achieving their fantasy and offering sufficient counterplay (Ahri, Lux and Bard come to mind). Riot's juggled with complexity creep in recent champion designs and reworks, and have succeeded in implementing fun, relatively simple kits in recent times, but the hallmarks of that original impetus for more kit complexity were CertainlyT's champions, who among other things are poked at for each having a long list of passives, conditionals and secondary effects, many of which don't feel particularly essential to their kit (even if they are, as is the case of Yasuo's crit passive, though not so much in the case of his original bonus flow generation). CertainlyT has had a major impact on League's design, much of it positive, but as he is a very experimental designer, his works are also prone to error, and those errors have had a larger effect on some of League's relatively recent design decisions as well.