Here's the thing about Malzahar. If you can avoid his Malefic Visions, don't stand in his aoe, and don't get poked down by his slience, you're good. The only reason his ult is so strong is because people let him infect them with Malefic Visions, directly or via jumping off the minion wave, stand far away from their tower, and act surprised when his ult goes off and he kills them. You get two dots on you, and good malz players will have their aoe down on you, so that's 3 DoT's going at once. It's a lot, but it's avoidable. Pretty much by any mid laner, in fact. Just don't stand close to something with malefic visions and hang back away from him, or where he can't safely ult you without being in tower range. It also helps if you can out-cs him, or have some way to push him back or punish him, like with annie (since she has mostly unlimited poke and high burst, due to her q farming refunding a lot of her mana) and she has a stun that can keep him at bay. Any popular mid right now can deal with malz, it's just that people don't know how to. A lot of people barely even know what malz does, let alone try to find counter play to him.
don't give up; I made malzahar cry as veigar, and this was before his buff that gave him stacks on assist, and before his surprise pick in the lcs. If you know what you're doing, you can beat malz as pretty much anyone.