(Warning: Long post)
CertainlyT didn't make Zed or Zyra, he did some small work on both but wasn't the main designer. They don't count as examples.
The problem with CertainlyT's champions (excluding Darius) is that they tend to do everything. They have no real weaknesses, or when they do, their kits have tools to allow them to negate those weaknesses.
I'm not going to mention Darius here because he doesn't follow the pattern of the other champions (plus, I don't personally play top so I'm not experienced enough to really analyse him.)
That leaves Thresh, Yasuo and Kalista.
Thresh does everything. His Flay alone is one of the most powerful abilities in the game (though yes, it takes skill to use well), but he also has a "dodge or die" hook (not as good as Blitzcrank's, but still there), a shield, a free escape for anyone on his team, an ult with massive area control, and a shield. He literally has so much going on on his kit that even if they reduced all his numbers to nothing and removed the poke he gets on his Flay passive, he'd probably still be the most-picked and most-versatile support. This isn't a numbers issue, his design has too much in it and can never be truly balanced while keeping all of the tools he has in his kit.
Other supports are good at one or two things, but Thresh does it all. And this probably the best of the three champions
Yasuo also has a lot going on in his kit, but his main problem isn't so much the overload but the fact that he has the tools to negate his weaknesses so well that he can effectively invalidate a lot of champions. He hard-counters many mage champions who are reliant on skillshots and use mana, while also having great damage, late-game scaling, and strong utility even if he's behind.
Riot love to talk about how abilities (and champions) should have counterplay, and one of the things that are often used as an example of counterplay is skillshots - which is true in most cases, but a champion like Yasuo can dash so often for free that he becomes almost impossible to hit with skillshots, yet he doesn't pay anything for this strength. Take for example a Katarina using Shunpo to dodge a skillshot - she puts an important skill on a fairly long cooldown by doing so. Someone like Ezreal goes one farther and also has a significant mana cost added. These champions can use their skill, at a cost, to outplay a skillshot. Yasuo gets to do it for free, with no cost and almost no cooldown. Furthermore, if there is something he cannot dodge (a skillshot with no minions near, or a non-skillshot projectile) he can throw up his wind wall to block it. This does have a long cooldown, giving it some risk, but the effect is lessened when added to his crazy mobility. Finally, for what damage does get through his first two defences, he has a third defence - a free shield - to block even more damage. He basically has three tools that are each strong against poke mages, all for free (while the mage needs to use mana to do their thing), and combined together they make him an absolute nightmare to play against as any kind of ranged skillshot mage. He basically invalidates an entire subset of the champion pool, and you are forced to pick something else in order to have a chance to lane against him. Again, all of this does require skill on the part of the Yasuo player - but after a certain level of Yasuo's skill, his opponent's skill doesn't really matter any more, because the Yasuo can negate almost anything the opponent can do.
Finally, we get to Kalista. Again, she has a lot of things going on in her kit. She has a delayed damage pattern, a lot of utility, and works very well with a support. That alone would have made a viable champion, but in addition to that she has a passive that gives her unparalleled mobility when near targets to attack. This has all of the same issues as Yasuo's mobility - it makes her almost completely immune to skillshots. Since she is free to hop in any direction and not just through enemies like Yasuo, she's even better at evading skillshots, since she can change direction at random, or even once the skillshot projectile is already in-flight. Yes, this takes mechanical skill, but again after a certain level of mechanical skill she can completely negate an entire class of champion. Her infinite hops also make her almost completely immune to champions with a shorter range than her, unless those champions can gapclose to her and kill her instantly (or CC her long enough to kill her.)
Again, this is a champion whose kit allows her to negate the skill of her opponent and to hard-counter a large subset of champions.
You'll notice that none of the things that I've complained about here are numbers or power levels. They are, instead, problems with the kit of the champions that make them almost impossible to balance, extremely frustrating to play against, and actually break several of Riot's own design philosophies (basically, having champions who hard-counter others to such an extent breaks Riot's goal that games should not be won in champion select.)
The balance team is left to try to clean up the mess, but it's really difficult for them. They can try to either massively reduce the numbers to make the champion seem balanced (like Yasuo, who is "balanced", verging on weak, but still retains all of his problems and is still heavily hated by the people who have to play against him), or they can try to nerf/adjust basic parts of the game for that specific champion to try to bring their power level down (adjusting Kalista's autoattack ratios, which makes her closer to "balanced" but doesn't change any of her hard-countering issues), but none of these changes can really fix the champions because the design is too overloaded and impossible to balance. The champions really need reworks to bring them in line, despite only being recent releases.
As for CertainlyT, he designs champions who have great thematics, well-designed characters, unique mechanics, whose kits feel fluid and fit well together. He has a lot of good ideas, but the problem is that he puts too many of them into a single champion, resulting in an overloaded mess, instead of keeping the unique ideas and spreading them out more over different champions. This isn't entirely CertainlyT's fault, though, since the rest of Riot's design team approve and champions and allow them to get added to the game, and also help with the design and implementation.
Also note that CertainlyT's champions aren't the only offenders; there are other champions with similar design issues. It's just that nearly all of his champions have them, and they are also more recent than most of the other offenders (where "Riot were new and didn't know any better back then" can be used an excuse.)
What I can't understand is how the designers can talk about Riot's design values, especially when talking about reworking or redesigning older champions, but the same rules are broken and ignored for (some) newer champions.
I don't really have anything to comment on the Morde rework. I'll wait until the changes settle a bit more and I see it on live before forming too much of an opinion.