X-Men 2 was a pretty good adaptation of God Loves, Man Kills.

I would love to see Messiah Complex, Second Coming and Messiah War, but I think it would have a better shot if they did animated movies of them like the DC movies. X-tintion Agenda would be cool after some character establishment, and Phalanx would be a cool big Marvel Universe event (since they f'd the Secret Invasion stuff) having people gradually become infected though the movies. But for an opener they really need to do the actual First Class some justice.

"...even the most ardent MCU fan has to admit to just a twinge of melancholy that this era of superhero cinema is over..."

You, sir, are mad. No. There is ZERO melancholy that the FOX era of butchering the X Men is over. Quite the opposite: JOY.

The X Men's worst and most fearsome foe is not Magneto, the Brood, the Brotherhood or even the Hellfire Club; their most evil and deadly antagonist is Bryan, The Singer!

I want the original 5 against the sentinels. The original purple sentinels. The villains are secondary to the team dynamics and the persecution of mutants.

I want them to properly introduce mutants and the X-Men first, then properly build up the characters and then add some of these awesome stories, specially X-tinction Agenda that was one of my favorite X crossovers.

They need to start with Sinister manipulating Bolivar Trask to trick him into creating Sentinels. So Trask outs mutants to the world and spins them in a bad light, telling everyone that they are the next step in evolution, which causes panic among regular humans.

The X-Men work as an outreach program for mutants to help them control their powers. They don't become a superhero team until the Sentinels start attacking mutants in the streets.

This is the best way to introduce the world of mutants to the MCU and establish the dynamic between humans and mutants.

Then they need to have Magneto come out of hiding and attack humanity by taking over a military installation and threatening them with nukes if any further attacks on mutants take place. Instead of a Holocaust survivor he is a survivor of a government testing facility that performs horrible tests on mutants and sometimes kills them. This way he still has the same motivations as he did when he was a Holocaust survivor. We can also get a younger version of Magneto in the current timeline like this.

After that, the 3rd movie should be about Sinister coming back out of the shadows and trying to capture Cyclops and Jean to make the most powerful mutant in history. Cyclops and Jean have a baby in this movie. When they beat him he infects the baby with the techno virus out of spite. He warns them that he was doing all of this because Apocalypse is coming and it's the only way to defeat him.

This sets up the next trilogy where Cyke and Jean send the baby into the future and Cable returns.

I think any story that involves time-travel is gonna a tough one to tackle