Apocalypse can't change the composition of his chemistry.
He can shape shift but element shift? Wikipedia admits that he has control over his molecules but only lists that again as a way to change his superficial configuration... Although it also says that he can "grow" jet engines off his person.
Here's the thing about Apocalypse.
If he fights to win, he wins.
Every one is dead.
And then he's sad.
So the big A doesn't fight to win all that often.
To service Evolution, he gets the light weights and intermediates to duke it out levelling up so that he has a little company on high.
Apocalypse is a telepath.
He says "Sleep" and the Hulk goes to sleep.
No, you're wrong, the leader is a shit telepath.
Onslaught totally pwned the Hulk back in the day.