In March of 2019, the Captain Marvel movie will introduce us to an alien race called the Skrulls. They are a shape shifting race who in the comics were the villains of the Secret Wars.
I believe the Skrull invasion already began and will explain how they were set up to be the next villain for the Avengers after they deal with Thanos.
The Skrulls in the comics are green-skinned reptilian humanoids with large pointed ears and red or green eyes. Their shapeshifting ability allows them to take the appearance but not the characteristics of other beings. This would allow the Skrull who took Bruce Banner's place to appear as him but not have the same personality. This is why in Infinity War, Iron Man points out the Hulk was acting differently than the last time they were together, which was during the Age of Ultron.
Avengers Infinity War opened with Thanos having killed what’s left of Asgard’s population as he looks for the Space Stone. He has Thor beaten, Heimdall laying on the ground, and is questioning Loki. This is when the Hulk pops up and begins fighting Thanos, with the Hulk quickly losing. Thanos then kills Loki after Loki attempts to kill him.
After Loki's death, Heimdall uses the Bifrost to send the Hulk back to Earth to warn the Avengers of Thanos. We next see something crashing into the Sanctum Sanctorum and that something is Bruce Banner. The movie wants you to believe the Hulk just turned back into Banner, but this is where my theory begins.
If you look back at the other Marvel movies involving the Hulk, Bruce Banner never remembers what the Hulk did. Some evidence of this is during Thor Ragnarok after the Hulk finally turns back into Bruce Banner, he tells Thor that he doesn't remember anything since they back fighting Ultron and Thor tells him that he had been the Hulk for at least two years. With this being the case, why would he now remember Thanos and the attack on the Asgard spaceship? He only would if the Skrulls switched out the real Banner with a Skrull copy to not only warn the Avengers, but to gain a foothold on Earth for a later invasion. Replacing the Hulk first would be smart since he is considered one of the strongest Avengers.
This is why the Hulk doesn't make an appearance the rest of the movie because if the Skrull did turn into the Hulk, he wouldn't have the same strength or durability and would die in battle, revealing the invasion early.
One reason I enjoy this theory and the potential Secret Wars story line the cinematic universe could be taking is that the Skrulls, while being a global threat, they aren't just one overpowered bad guy. You would never know who is secretly a Skrull and the team wouldn't trust each other, leading to more drama and a better story. And yes, I do love the idea of Galactus or even Dormammu as the next big bad. I think they would be better served after the Fantastic Four are brought over from Fox and Dormammu as a Doctor Strange only villain.
The Skrulls have been an enemy of the Fantastic Four in the comics, with Mister Fantastic being the one who discovers a way to identify Skrull shape shifters. This would be a perfect chance to bring them in especially with many of the original Avengers leaving soon.
As a bonus for reading this theory I thought I would include who I feel would be the perfect casting for the Fantastic Four into the Marvel Cinematic Universe.
Mister Fantastic and the Invisible Woman should be none other than John Krasinski and Emily Blunt. The real life couple showed in the movie A Quiet Place that they have great on screen chemistry and both have been in the running for Marvel heroes in the past. The Human Torch can only be Zac Efron. He has the muscles, charm, and personality to play fun and Sue Storm's brother. Finally, I would pick John Cena to play the Thing. While he isn't the best actor, he has been in more and more films recently—mostly comedy. He does have a role in the upcoming Bumblebee film. He has the size for the role, he just needs to play Thing less comically.