Why don't people pick more AP champions? If people did that, I am sure that everyone would realize that Malphite is balanced.
Using the pick/ban phase to pretend you're the balancing department is kind of a waste more often than not.
Looking at win-rates, champion performance, and a wide range of stats you're usually left with the information that banning out champion X will simply mean champion Y, that's 0.05% worse, is still available. This difference in power continues throughout the entire roster. If an opposing team is well-versed in the top meta picks, banning the "OP" champions usually only nets you an extremely minuscule advantage. If they wanted to play the top pick and their fall-back is the 10th best pick rather than the 2nd best you might get something out of it, but odds are that isn't the case.
However: If you want to run, say, a full-AD composition and Malphite is essentially the only counter that's widely played: Using a ban against him is extremely useful in the pick/ban pahse and greatly increases your chances of winning.
Which begs the question: why run an AP champion to net a 0.05% advantage in picks/bans rather than ruining the enemy's chances of stopping the team comp you want to run?