I would have thought Apocalypse would have garnered a higher spot on your list. I mean he's touched so many X-Men during his comic tenure. Wolverine, Angel, Polaris, Gambit, Sunfire, Cable, Cyclops, Jean, Iceman and even villains like Mystique, Exodus and basically created your number 1, Mr. Sinister... He conquered an entire alternate Earth, and is the cause of several large story arcs even after his death... How did he die again?
While yes, he had touched allot of Xmen. Only merged with one though, but made horseman of the others. And while he did create Sinister - who is clever if not a bit too scientific. When written well (Gillen), he is more than just mad scientist. Poccy isn't all that impressive as a villain. He's got power and tech.
Apocalypse does his thing, fails, then disappears. Wash, rinse, repeat. While formidable when awake and taking on Xmen or making them horsemen, the end result is the same. He fails, he goes to sleep. His goals aren't even that unique. Wants to rule the world. Thats it. Maybe there is more depth to him but I've never seen it.
He reminds of Godzilla without taking over he world and having horsemen. Godzilla's main thing is to cause havoc. He wakes up from his watery nap, walks to whichever continent (usually Asia, every where in new film), and destroys stuff.
If he's a good guy, the excuse is he's helping save the world he lives in, and when he's done he goes right back to the ocean for his nap.
If he's a bad guy, somebody woke him up and he's grumpy (usually the metaphor for how we should not test nuclear weapons, etc). He walks around destroying stuff and then is defeated (not killed), and is dumped back into the ocean where he can continue his nap. (Once he was tossed into space).
A long way to say one trick pony.
I suppose the effects Apocalypse has caused the Xmen should bring him further down on my list. Even so, the Xmen don't talk about it, a passing line maybe. There is no real aftermath or consequences. It's wrapped up and put aside.
The only character they really tried to do something with and it boring was Cyclops when he merged with him. The idea was interesting though, merging and seeing how a character deals with it.
I dunno how he died, and I suppose he'll come back. I think the fact they're trying to do something with the character via Evan is good on Marvel's part.
Thats why he is where he is on my list. Looking over my list - I appear to be partial to the more "thinking" type villain. Ones with plans with plans with plans. Exception of DPhoenix - no plans really, other than selfish ones .. still its a plan of sorts. But the power alone is quite impressive.
Here's an idea - have Apocalypse wake up when he knows the Phoenix Force is making a trip to Earth and have him harness it as his own. Though in theory there is no more Phoenix via Wanda and Hope. Still, Marvel changes its mind all the time.