I didn’t quite follow the comic but I managed to watch the older X-Men series when it used to air regularly on Fox affililates. However, I remember an episode where a mutant thought he found Apocalypse’s weakness and that when he tried to exploit that weakness, Apoc. laughed it off and said something like, “Not even the Babylonians with their arrows could do me harm.” My question is why didn’t he just take over the world way back when?
Hm. Here’s some ideas.
- Gilamesh (eternal) probably whooped up on him.
- He didn’t want to back then.
- It wasn’t in the script.
If you’re being serious, I’d say one. Personally, I’d opt for three. 
IIRC, he was busy just kickin’ it in another dimension somewhere. Though that thing about Babylonians seems to blow that out of the water. OTOH, wasn’t he worshipped? Maybe he did all but rule the world but got bored and left. I mean, what was there to do back then (that’s permissible by the comic’s code)?
Don’t forget that the X-Men TV show didn’t really accurately follow the comic. That’s one big reason.
Also, check here for more information on Apocalypse.
But, the biggest reason that Apocalypse didn’t take over the world was…because he was a bad guy, and bad guys never win.
