Here's the problem.
First, the Q nerf this patch was a revert. They never officially added it to patch notes, but his Q animation was significantly accelerated in the MYMU.
Second, his E does more of your HP than it did pre-rework, but only if you try to punish him for lazily using it to deal damage, this is mainly due to the Q refresh of the ability and the voidling power shift. If you are afflicted by E, then you are in an even worse spot than previously.
Last, having to time your abilities doesn't increase the window of opportunity, it only restricts the malzahar to a pre-designed window of kill potential, while increasing the breadth of his damage. It's no more difficult to play around than a yasuo's 3rd Q. You stack up your W, then go, W, E, Q, W, R. If they back off by Q (and it misses), then your W is stacked again for the next fight. If they get hit by Q then they can't flash/dash, leaving them open until you press R.
Seriously, the only difference between the two kits (from an AP prospective) is that his base and flat damage which was lost on his Q,E, & R, were put onto his W.
The rework attempted to "fix" the champion, somehow, by changing the number of mechanically useful abilities from 3 to 5 for AP malzahar (they added the AP voidlings and the general purpose spell shield). A good malzahar player could make some mechanical use of his passive and W before the rework, but they were extremely situational and player dependent. His W could be used as a zoning tool, because despite not doing a dangerous amount of damage to moving enemies, people stick to the "don't stand in the fire" mentality. His passive worked as an impromptu spell shield against single target skill shots, like blitzhook, thresh hook, ahri charm, karma Q... well the list of useful blocks is actually pretty small.
AD malzahar utilized his passive as the primary damage tool, and then treated the rest of his kit as utility. No need to elaborate much on this point.
The only difference in "counter play" really was the shift of his damage to his voidlings, which really don't have any kind of "counter play" they have "mechanical counters". A list of champions who by design of the champion, not the player's usage of them, can easily remove the flat damage provided by the voidlings.
Call me crazy, but i wouldn't consider riot tailoring counters to be "counter play", on the basis that it's not dependent on the player to counter the action, it's dependent on the champion having a tool to deal with the action.