If by some miracle FOX decides to agree to let Marvel use its characters then the two that would best fit would be Magneto and Doctor Doom.
The movie success for X-men maybe good for the moment, but they cant go on forever, and eventually it would make sense for FOX to give in to Marvel. Fantastic Four isn't even doing that well at the box office seeing as it has barely made what was expected, even Kate Mara's Invisible Woman thought it was a joke. There are also some actors from FOX who agree its time to share characters like Toby Kebbell's Doctor Doom, and even Hugh Jackman's Wolverine.
Giving these characters origin stories in the MCU is tricky but I think there are a few loopholes that could work.
First off, not as Victor Von Doom, because its been used in both FOX movies and it just does not sound like a real person's name. I would go with Victor Van Damme, Ultimate Doctor Doom's name which sounds alot more real.
Secondly during each FOX incarnation of the character, Doom was from Latveria but was never in charge of it, which could give him some more comic roots. Also, Doom developed superpowers during each time the Fantastic Four got theirs which could contribute even more to the comic roots. But how to introduce Doom into the MCU without the Fantastic Four?
Well in the comics Reed Richards and Victor were rivals in college which led to their rivalry over the years, maybe this role could be replaced by Tony Stark. If that were the case then in college they would work on a project together which results in Victor being scarred and blaming Stark. Victor would then spend about ten years doing unknown activities, until he returned to Latveria and led a rebellion against the King, where he would then become their leader.
Through his leadership Latveria would become the second most advanced country in the world, second only to America. Yet this would not be enough for Doom as he wanted more power, so he would use his technology and army of robots to wage war against the Avengers.
This design at the top (heavily inspired by the classic Doctor Doom, with a little bit of modern Sci Fi) is from Darthdestruktor of Devianart. The idea is to make him distinguishable from the Fox versions, and yet to have him recognizable as Doom. Tricky, but I think a design in that spirit could work. He would have the Helmet, Green cloak, and Body armor.
Besides its not like he's only a Fantastic Four villain, Doctor Doom has clashed with the Avengers on various occasions, but since his origins are with the Fantastic Four his rights go to FOX for the time being.
My pick for the actor would be William Fichtner
First off, not as Erik Lehnsherr.
Yeah Quicksilver was in X-Men and in Avengers: Age of Ultron but you’ll note he was never called Pietro in X-Men, and was actually named Peter, so that allowed some room for different use. That double use was possible because Quicksilver is part of the Avengers as much as the X-Men.
Back to Magneto. In the comics, he went by many names. This means he could be introduced by another identity than Erik “Magneto” Lensherr. My pick would be to go with Max “Magneto” Eisenhardt. Nitpicky, but that could create a loophole in the legal use of the character.
This design at the top (heavily inspired by Clay Mann’s design for Age of X) is from Lucas Boltagan of Devianart. The idea is to make him very distinguishable from the Fox version (so no red, or purple), and yet to have him recognizable as Magneto. Tricky, but I think a design in that spirit could work. He would have the white hair, explained the way than for Pietro : high stress and body stimulation.
Rather than being a mutant, maybe Max is a Inhuman, or even a human augmented by Inhuman biology, who initially does not possess powers but after going through the change gains them. Also, Instead of controlling metal, they could play with the idea of Magnetism and force fields (again, similar yet different).
Magneto’s WW2 history is important to the character is important, but impossible in the MCU timeline. And remember that his WW2 origin was revealed much later in his comic history. So instead of being a WW2 survivor, he could have fought in a war in Eastern Europe (Sokovia or another country). We all know there are terrible wars and atrocities happening in those regions.
The “Mutant leader who would do everything for his people, at any cost/anti-hero” angle has been explored well at Fox, so here I would go with the earlier traits of Magneto, the bad guy, the terrorist almost. Not my favorite iteration of the character, but there is no point in redoing what Fox has already done. He would have his reasons, sure, similar to his X-Men version, but it would be clear here that he is a bad guy, not an anti-hero.
As for his ties to the Twins, my story would be that he was good friends with their parents, and at one point even fell in love and went so far as attempting to seduce Magda, the Twins mother. The Twins father Django Maximoff would stop Max and tell him to never come back. When the parents died, Max would watch over the Twins from a distance.
How does he meet the Twins (or just Wanda if Pietro isn’t brought back) ? If he is an Inhuman/Artificial Inhuman then my guess is he goes on to work with the High Evolutionary, who augmented the twins using Inhuman biology. After years of preparation the time had come for Max and the High Evolutionary to enact a plan for global evolution, and during this he meets the Maximoff's. Then he and the High Evolutionary would convince the Maximoff's to join their side as part of an alternative Brotherhood, but after discovering the savagery of their plans the twins would rejoin the Avengers.
My pick for the actor would be Jeremy Irons.