It occurs to me that Marvel has just obtained a host of villains that are suitable for "Phase Villains" due to the merger.
Galactus is a thing that can happen now, as well as Dr. Doom, Annihilus, and numerous X-villains. Pretty much all they had up to this point was Thanos.
What were they going to follow him up with? MODOK?
It's entirely possible that the best thing to come out of this merger is that Marvel gets a lot of its more interesting villains back.
Plus, we get the possibility of Namor, Silver Surfer, and the Fantastic Four again. Wolverine could also make his way to the Avengers as well once they kick off X-Men.
Spider-Man has some cool and memorable villains, but I'm not seeing them really being global threats for the most part. That roster could work for single movies, but not for Phase type villains that could really bring together a series of films.
I'm thinking mutants will be worked in as a new thing for the most part. There were probably a handful that existed prior to the MCU, but something happened to create a lot more. I'd guess the X-men will be mostly teens or young adults with few exceptions. The MCU is already setting up mutant powers being something the public would see as a threat. Civil War did a pretty good job of planting the seeds of the public fearing powers in general, and X-movies could pick that up and run with it.
That would explain why they weren't there for the big events going on prior to their debut.
After watching the Infinity War trailer again, I'm kind of wondering if they have the balls to kill off Peter Parker and replace him with Miles in the next Spider-Man movie?
I could see that as a really good reason for Tony to stop being Iron Man without killing off Tony Stark.
I've also heard rumors that Hugo Weaving is in talks to reprise Red Skull again, and maybe even have a cameo in Infinity War or the sequel.