Malzahar's Disease is Holding Him Back
TL;DR: Malzahar's base numbers are too high, DoTs are unfun, Malzahar suffers as a viable pick due to the inability of balancing his E. Suggestions at the end.
Malzahar sucks. As a champion, he feels useless. He's frustrating as hell to play against. And it feels like half his kit doesn't even exist--it's just his E and R running the show. My idea? His E (and all targeted DoT based abilities) are inherently broken. They are impossible to balance. There is no counterplay, no interaction. If the enemy is able to ignore the DoT, then the DoT ability is incredibly useless. If the enemy isn't able to ignore the DoT, then they have no room to strike back at Malzahar. Swain also has this problem, although I feel like that's a whole 'nother can of worms.
Point and click nukes, such as Annie's Q, are gated by the fact that the damage comes out in one burst. On one hand, this is beneficial--they allow for bursting and unexpected damage. On the other hand, this is extremely detrimental--during the entirety of the cooldown, the champion is much weaker. These abilities fill a niche--guaranteed, targeted damage. They all have their drawbacks: limited range, cooldowns, cast time, limited damage, et cetera. Which drawback they get depends on the rest of the kit. For instance, Annie's Q is up a lot, but has an extremely short range (for a mage).
But point and click DoTs? They fall into an extreme binary: either the enemy can fight back, or the enemy can't. Sure, with point and click nukes, a similar situation can occur, but at least the enemy champion is left weaker for the entirety of the cooldown. With point and click DoTs, however, you're left with deciding between attacking while the DoT is on you (and potentially taking more damage than you anticipated since it's hard to tell how much damage a DoT will do until it's done) and attacking during the incredibly small window while the DoT isn't on you and is on cooldown.
Looking at base numbers of other champions, most point and click nukes are between 150-260 damage. Usually most of them fall around 200-240, with only certain cases being on the lower end. Kayle's is 260, which was the highest I could find. Anivia maybe has higher, if you consider the double damage on E, but that requires a minimum of two abilities. Likewise with LeBlanc's Q. Looking at base cooldowns, and it's almost always between 6-12 seconds. A few fringe cases, which is balanced by the respective kit.
Malefic Visions, Malzahar's E, compensates for the lower end of the binary by having an insanely high base damage, as well as (supposedly) making the voidlings attack whomever is afflicted by the ability. This doesn't solve the binary at all. Instead, it simply shifts it. More of it is on the too strong side, too little is on the too weak. Malzahar's E does 320 damage. (282 damage on Swain E.) Kassadin would almost have to Q twice in order to do the same base damage on one Malzahar E. And the scaling is far from bad for both of them: 80% for Malzahar, 96% for Swain. Malzahar's E cooldown is, admittedly, rather high at rank 1 (15s), but goes down by 2s with each rank, ending at the very top of the power curve: 7s. Throw in some CDR, and it's always up.
This isn't even considering that it's just unfun to play against. I'm of the opinion that DoTs in general are unfun, but Malzahar's (and Swain's, to a lesser extent) is an extreme case. There is no way to dodge it, except for attempting to wait until he uses it on a minion wave, and even then you have to be careful with you positioning. The damage is done to you over time, so it's hard to get a grasp of how much damage it will do, leading to cases where you may flash without realizing you're dead, or other things. It leads to too many messes with too little counterplay.
I'm not attempting to claim Malzahar is OP. In fact, I think he's in a very bad spot right now. He is easily shut down due to jungler ganks (due to his incredible dependence on level through his E and Q), his teamfighting is hilariously bad with his R being useful only for self-peel due to how he's trapped in a channel at a short range, and while his mid game and pick potential is incredibly high, he struggles to even get there unless he snowballs from his lane harass.
My suggestion? Either change his E to be fundamentally different (for instance, something like a Cassiopeia Q where it applies Malefic Visions to everyone hit by it), to switch the power of his kit more towards his Q, or to enable his E to be much more interactive with his Q and W. A combination thereof is also completely viable.