These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Crack Pairing: Quicksilver & Storm, Gambit & Lila Cheney, Boliver Trask & Moira MacTaggart, Exodus & Dazzler...they really go all over the place with this. However, the more official ships are acknowledged, even if they go a bit differently in this universe. For example, Jean ends up with Wolverine, since Cyclops was never an X-Man and they never met until after the cross-over begins; however when Scott, who was an agent of Mr. Sinister, makes a Heel-Face Turn in part because of meeting Jean after she was captured by Sinister, the two end up back together.
Apocalypse himself, having destroyed most of Asia and Russia and committed mass genocide in North America. The point of the cross-over is what Apocalypse would be able to do unchecked by Xavier's X-Men.
One example stands out above all others. The Generation Next team member Vincent has the power to turn into a liquid or a gas (and maybe other things, the exact nature of his power is never explained). At one point, the GN kids are infiltrating a concentration camp. Husk gets inside by posing as a human prostitute hired by one of the camp bosses. She carries Vincent, in his liquid state, with her in a flask. After the camp boss blows her cover, he decides he wants a drink before he kills Husk, and drains the flask containing Vincent. Hilarity Ensues.
True Neutral: Angel does his best to stay this. Until Apocalypse's soldiers pull the plug on his club. Oh, and take Karma to pens. After this he is Neutral No Longer.