First, as I explained, the Acolytes wouldn't be an actual faction for this movie. They would be there in the background so Magneto can leave the Earth and create Asteroid M, which sets up the next X-Men movie.
So now we're down to three factions (not including Mags - though he'll need some story time - which is why I like my "I'm leaving, want to come" story).
You have to know that Mystique will be in this story. There has to be a reason why she took Wolverine, so it's either to be able to turn him over so he can become Death, or so he can be with her on her team (Brotherhood).
Of course Apocalypse and his Horsemen will be a "faction". He and they are the villains, so hopefully you can agree to that.
And of course Xavier and this new team of X-Men will be the protagonists.
You're right that it's possible that they could have Magneto as the leader of the Brotherhood, but haven't we been there, done that? Makes much more sense to me to have that go over to Mystique now, while Mags is looking to leave (or set up Genosha), which sets the events for the next movie. It also gives a way to get Quicksilver aligned with Magneto.
It's hard for me to believe that they will have more than one known character as a Horseman. If they did, like turn Wolverine and Mystiaue and Magneto into Horsemen it would take so much away from their characters. You just can't give enough development time to all three (or four - if the 4th Horseman was also a known character, like Havok). No, making it just one makes sense, and as I wrote a while back, Wolverine makes the most sense (with Archangel being the next best choice).
Sure, maybe he won't be called "Death", but why not? Why wouldn't Apocalypse call him "Death"? It couldn't hurt...
I also don't see Magneto or Mystique "joining" the X-Men, nor did I say that. But likely Apocalypse will be such a huge threat that all of these "factions" will need to join together in order to defeat him. That just makes sense...
It's basic story telling.
1. Show each "faction" doing their own thing, motivated by whatever it is that motivates them. Mystique seems motivated in freeing and protecting her mutant bretheren. Magneto seems motivated with ruling/defeating the humans, though I could easily see him realizing that there is no winning, so instead isolating and protecting him and the mutants that join with him. And Xavier will be bringing them together and training them.
2. Show the threat of the main villain. Obviously the story will get to the point where it is seen that Apocalypse and his Horsemen are such a global threat that everyone (human and mutant) are in peril.
3. Bring all of the non-villainous factions together to fight against the threat. It's an enemy of my enemy plot.
4. Have the "factions" defeat the villain and then go their separate ways, again motivated by their own things...
This is what I expect from this movie...
Killed?
