"Malzahar is a bad champion because his ult can be countered by QSS and he is immobile"
counters a lot of champions:
(his ult can be removed, so QSS is an option if you are AD)
(removes the fish)
,
, and
(Malzahar is not the only champion with suppression)
(That crippling slow can be removed by QSS - this includes the attack speed slow)
(the ult)
(the ult as stated by an user on this thread: http://boards.na.leagueoflegends.com/en/c/gameplay-balance/Y2otPTfY-everyone-knows-you-can-qss-fioras-ult-right )
Any CC
As for the immobility... This is a problem for many champions.
for example is immobile and he is one of the most popular mid lane champions, and he doesn't even have that much range. Immobility is not a problem for many champions that are or were popular

Honestly, though, I would rather want Malzahar not to become popular. Why? Because if he was popular, he would be nerfed. Just see what happened with Viktor. I want him to continue as he currently is so that I can enjoy him at rankeds, and carry games with him. I know that he is not as bad of a champion as people say that he is. However, it still bothers me that people mock him without even trying to master him.

never forget (mobility issue solved)
because Malzahar just synergizes incredibly well with this item
because of CDR and Malzahar has mana problems
because Morellonomicon is not enough to solve Malz' mana problems, plus he needs HP to survive the focus and initial burst
to survive against some situations, for outplay potential, or for when there is a Zed/Karthus/Fizz on the enemy team
because well, Malzahar is an APC
because sometimes Sorcerer's + Liandry does not give enough magicpen against tanks
--->
completes build with
and
.
for the magic penetration and early powerspike then I build Athene's Unholy Grail for the CDR and because the passive is better for solving mana problems when compared to Morellonomicon.
"weak early game"
"stack armor"
"just CC him"
rushes QSS, this means that he is not rushing
, even if he builds this a second item, his powerspike will be delayed. He can build this after, but then it is not lane phase anymore and Malzahar can take advantage of this to snowball his team and carry.
.
or
and
.
you are required to use Ignite against him due to his ult. Without Ignite you lose trades due to his insane healing. Ignite is also required against
or
on the enemy team. You have to take into account a lot of factors, though - Do your allies plan to use Ignite? Are there any dangerous assassins on the enemy team?