It is inevitable: the X-Men and Fantastic Four are joining the MCU -- sooner rather than later. The Marvel Universe will be complete again. It is tempting to say "Let's just bring all the characters in at once, all at the same time, so we can get the FF and X-Men in our MCU fast!"
But that's short sighted. That's not how Marvel has been doing things lately. Black Panther has been teased since Iron Man 2 and Avengers, with him appearing in Captain America: Civil War long before his solo came out. Spider-Man was also introduced in Civil War. The Planet Hulk storyline was adapted in Thor Ragnorak. Story-lines and characters can pop up in films you wouldn't expect, and, so we don't get bombarded with a dozen solo films introducing the Marvel/Fox crew, it might be wise to slowly introduce the new characters in other films first before combining them all.
There are numerous way the Marvel Fox characters can be introduced into the MCU.
10. Adam McKay and Silver Surfer
It has recently been confirmed that director Adam McKay (The Big Short, Vice) is interested in directing a Silver Surfer movie. The Silver Surfer can be the ideal way to introduce the cosmic forces of Galactus before, potentially, the character appears as the antagonist of a future Fantastic Four film or the like.
At the very least, a Silver Surfer film can expand the cosmic side of the MCU in ways that prior films can't. It can offer a story of power beyond that of Thanos, in ways that establish an almost cosmic-horror element to the MCU: forces so incredibly powerful that your best hope to win is to pray they don't notice you. Yet.
9. Storm In Wakanda
In the comic, Storm for is married to T'challa for a while -- the Black Panther. Storm is arguably one of the most iconic women of color in comics. When the Marvel Fox characters come to the MCU, it might be wise to introduce her in a sequel to Black Panther.
Ryan Coogler has in the past expressed interest in playing with characters outside the immediate Black Panther cast. He wanted initially to bring Spider-Man villain Kraven the Hunter into the sequel. It isn't a stretch to argue that Storm, who already has a history with Wakanda, might make a first appearance in the MCU in the country of Wakanda.
8. Sokovia Becomes Latveria
The MCU featured the civilization of Sokovia back in Avengers: Age of Ultron. By the film's end, the country was ravaged by Ultron. We never did learn what happened to the country following that event. Is it that unlikely to imagine that Sokovia might've been conquered by a mad warlord?
It seems inevitable that the MCU will feature the glorious villain Doctor Doom in some way, and what better way to show how dangerous he is than to tie him in as an opportunist rising the ranks following the disasters beset in the prior films? Perhaps the former Sokovian people even thrive under Doom, thus inspiring the fierce loyalty of his people.
7. The Fantastic Four Gain Their Powers Using Thanos's Tech
While the fallout of Avengers: Infinity War has yet to be explored, Thanos left quite a lot of technology behind following the Battle of Wakanda. Much like how The Vulture salvaged the Chitauri tech in Spider-Man Homecoming, a scientist like Reed Richards might salvage Thanos's tech -- and find himself in over his head.
While there can be any number of advanced technology failures that afflict the Fantastic Four with their powers, it seems like a potentially good way to tie in Marvel's First Family to the MCU. After all, it isn't like the Marvel/Fox films have done the Richards any justice yet.
6. The Inhumans And Wakanda
Forget the Inhumans were in the MCU? Don't worry. Most people probably do. The Inhumans and Wakanda were heavily tied to the Fantastic Four prior to them becoming independent storylines. While both the Inhumans and Wakanda have been introduced already, it seems possible that, when a Fantastic Four movie happens, they might tie the film with one or both of these previously established worlds.
Of course, the inevitable FF film might focus move onto something unexplored, like the Negative Zone or Latveria, but the possibility of Reed taking a trip to Wakanda (especially as an advanced scientist himself) cannot be dismissed just yet.
5. Spider-Man And The Human Torch
Of course, it is possible that the FF might be first via an appearance in a prior film, and what better film to introduce the FF than in a Spider-Man film?
The inaugural issue of Amazing Spider-Man featured Spidey attempting to join the FF. Since then, he and Johnny Storm, AKA the Human Torch, have been the best of friends. With the MCU Spider-Man films continually linking Spidey with some member of the MCU (Tony Stark in Homecoming, Nick Cage in Far From Home) it seems logical that, rather than pair Spidey with a mentor figure in his third outing, they link him up with a peer.
4. House Of M
Scarlet Witch has not been having a good time in the MCU. With the love of her life snuffed out before her eyes, to losing her brother, to being blamed for tons of horror and death, it seems she might just want to reshape the world.
The House of M storyline offers a lot of possibilities to the MCU, but one in particular might be perfect for a few...retcons. More specifically, the retroactive awakening of the Mutant Gene, the resurrection of Quicksilver, as well as the potential resurrection of their father: Magneto.
3. Alternatively, Mutants Were Hiding The Whole Time
An alternative to the prior theory, though, is that mutants have been in the MCU the whole while: humanity just forgot about them -- though not without a little help.
Though it may draw comparisons to X-Men First Class, it would be interesting to see a period X-Men piece show Professor X and Magneto working together to combat some mutant threat, which would lead to, potentially, Professor X using his abilities to erase the world's memory of mutant kind. While it may seem odd, this might offer a good reason why mutants have remained forgotten for so long, as well as potentially justify humanity's fear and hatred of them. After all, if you just remembered the next stage of human evolution was hiding under your nose, you'd be a bit suspicious too.
2. Deadpool Sees Through Continuity
Of all the Marvel Fox characters to be introduced in the MCU, Deadpool seems to be the only one potentially aware of the change at all. As he is now a time-traveling madman with the ability to comment on casting decisions (and Thanos), it seems improbable that he wouldn't know about Disney buying Fox.
It also seems like a good way to keep Josh Brolin in the MCU family, as he'd be both Thanos and, presumably, retain his role as Cable.
1. WWII And Wolverine
Of all the possible ways the Marvel/Fox characters can be introduced in the MCU, this one is the most appealing. It seems impossible to replace Hugh Jackman's immortal mutant Wolverine. Even more so, it seems impossible to figure out a way to relay the mutant's extreme age in a few films. But one way to do it is to show a multi-generational story of the world's most famous mutant -- one that has him cross paths with Captain America himself.
Chris Evans seems reluctant to leave his most iconic role, so it wouldn't be a stretch to say he'd stay on for a film which will allow him to take on the Red Skull one last time with Wolverine, potentially allowing Wolverine a way to carve a niche for himself as one of the most savage characters in the MCU.