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.
YMMV: Age of Apocalypse
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.
Complete Monster: Apocalypse himself is one of these in this story, having destroyed most of Asia and Russia and committed mass genocide in North America. Though Holocaust (as the name would suggest) is hinted at being even worse.
Apocalypse is a Complete Monster in normal continuity; the point of the cross-over is what Apocalypse would be able to do unchecked by Xavier's X-Men (it's strongly implied that Magneto's X-Men were never as effective under his leadership and this in turn paved the way for Apocalypse's rise). However, Dark Beast is a good example of a character who is a hero in normal continuity who is an absolute Complete Monster in AoA. It's shown that even other villains are creeped out by the sheer joy the Dark Beast takes in conducting experiments on live subjects, including both humans and mutants.
Point of order: The only reason Apocalypse rules in this reality is because the psychic backlash from Xavier's death awakened him 20 years early. He "realized" Mutants were coming along faster than expected (he didn't know the mutant battle was conducted by people from the future), so he made his move long before the world was ready for him.
Ensemble Darkhorse: Blink, though it still took her five years to cheat death and get a book.
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.