How would you introduce the FF4 and X-Men characters now that Disney bought them back?

Fantastic Four: Reed, Sue, and Ben are fresh out of college while Johnny is a high school senior. They have been given a grant by the Baxter Foundation to investigate the Negative Zone Reed has recently discovered. I wouldn't introduce Doom just yet but maybe the FF can fight Annihulus or someone.

X-Men: Mutants have kept a low profile for centuries but recently, more and more of them have sprung up and the next evolution of humanity has begun. People are scared and violent; in some cases, the fear of mutants is warranted while other times it isn't. Xavier's School for the Gifted has faculty to deal with such situations.

Deadpool: He's out of the mainstream MCU mostly but can come and go as he pleases. He knows he's a fictional character after all.

I would do the FF VERY easily. SHIELD detects an incoming energy signal in near Earth space. They call in Stark for analysis and tell him the energy signature matches that of Reed Richards experimental hyper-drive. Stark says he always thought Reed Richards was a myth. The SHIELD person (please let it be Coulson) explains that in 1963, Reed Richards was working on space travel to win the space race and, when the government was going to interfere, he stole his own prototype and launched it with his best friend, girlfriend and her brother as the crew. Soon after they left Earth orbit, they engaged the experimental drive and promptly disappeared. Assuming all hands were lost and to avoid the embarrassment that a scientist and 3 civilians were able to steal an experimental spacecraft, the government never owned up to the story and the whole thing became a myth.

The ship crash lands and SHIELD goes to intercept, expecting to find 4 55 year old dead people. Instead, well...you know what they find. We find out that the ship did not explode (obviously) but had been shunted into an alternate universe Richards called the Negative Zone. Because it was an uncontrolled entrance into the Zone, they spent 2 years there and not 55. The uncontrolled transition, in addition to a bombardment by cosmic radiation gave all four different sets of powers (shocking, I know). And now these 1960's people have to adjust to a 21st century world (a fun part of this would be everyone assuming Reed Richards would be way way behind the times in terms of science only to find he catches up and surpasses them in a period of days).

Meanwhile, in Latveria, sensors trip by the detection of the radiation and a tomb opens. We find that Victor Von Doom, who Reed had known until college and had left school after being scarred in an illegal experiment KNEW that Reed and the gang did not die (and may have sabotaged their drive to shunt them away) and, as he still wants Reed to die at his hand, ....

They could choose to keep the X-Men in a separate universe and bring FF4 as a pre existing team you simply have not heard much about yet. Reed Richard should be a peer of someone like Stark so I don't think they should be young adults like the last FF4 was.

I wouldn't do it in "Infinity Wars", there are too damn many characters there already.

How would I do it? Well, lemme tellya... I'd start with a Fantastic 4 film set in 1961. I'd avoid the comedy and quirkiness of Guardians of the Galaxy or Thor:Ragnarok, but keep it light and funny, in the spirit, and keeping the tone, of the original comics. Think Howard Hawks, Preston Sturges, Billy Wilder...

I'd briefly show the team's origin, probably while the opening credits roll, and then pit them against Dr. Doom and the Sub-Mariner in an exciting and unpredictable adventure. End by revealing that this is not the 1961 of the MCU.

Post-credits, something Thanos did in Infinity War would be shown to have had the effect of merging the two universes, similar to what happened recently in the comics. And just like the that, the FF, Doom, and Namor are in the MCU, and very much fish out of water, being that they are from a screwball version of 1961.