In May, The Avengers will hit the big screen again in Age of Ultron and it's to be assumed that results of that movie will lead into Captain America: Civil War. My guess is that we will see a ton of Marvel owned heroes and maybe villains popping up to help the Avengers fight Ultron and all of the robots and tech he will be controlling.
The good part is that the movie is more than likely going to be amazing. The bad part is that when Captain America: Civil War comes out that there are going to be a few key moments that are going to be missed. Chief among them is Spider-Man unmasking in front of the world. The separation of characters isn't a bad thing because the writers for the Avengers franchise have done a great job staying as close as possible to the source material without compromising the story or characters too. The disappointing thing is all of the moments, rivalries, and stories in comic books that we will never see because the companies snatched rights and won't play nice with each other.
Wolverine vs. the Hulk:
Of all of the Hulk's rivals, Wolverine is easily the most savage. Sure Thor is in Hulk's weight class and Iron Man has all of the armor, but no one goes at the Hulk like Wolverine does. Wolverine doesn't have the strength to go punch for punch with the Hulk, but what he does have is the skill and sheer ferocity to go twelve rounds with the Hulk and then some. What makes their rivalry and fights so special is The Hulk is one of the few people that Wolverine can go full berserker rage on without feeling bad for what he's doing; and The Hulk can actually hit Wolverine without breaking him. They both consider themselves monsters, and when they fight they certainly treat each other as such. There isn't a person in the Marvel Universe that can give the Hulk a fight like Wolverine can, and does. Hopefully one day we will all be lucky enough to see the two of them square off in a movie.
All out intergalactic brawl
I'm sure that in some way we will get a Marvel space war. It's almost a guarantee with how well Guardians of the Galaxy did and the fact that almost everyone loves space sci-fi movies and fights. But what's a giant space brawl without Galactus and the Silver Surfer? Galactus and The Surfer are arguably the biggest dogs in a space fight. I mean, one of the guys actually eats planets and is as old as (maybe older than) the Galaxy, and the other is his herald who has actually beat the guy who eats planets. Two of the toughest guys on the planet who won't get to fight Earth's Mightiest Heroes, the Nova Corp, or The Guardians of the Galaxy.
Then we have the Shi'Ar empire. The Shi'Ar are more than just their bird-like species. The Shi'Ar Imperial guard is made up of a bunch of different races of warriors (Gladiator, Fang, and Starbolt to name a few) all with different powers and looks. It would be great to see them in an all out brawl with The Avengers and The X-Men.
Lastly, we have the Skrull Empire. A warrior race who live to conquer and bring other planets and races under their rule. Not only do they continually try to fight the people of Earth and almost won and took over Earth during the "Secret Invasion," but they have a lifetime war with the Kree (another race of aliens that tried to take Earth for their own). The Kree have also been introduced to the Marvel Universe recently and it is going to be a shame that we won't get to see them interact or see the "Kree SKrull War."
Dr. Doom and Dr. Strange "Triumph and Torment"
While Dr. Doom is well known for being one of the two or three smartest people in the Marvel Universe, people always seem to forget that he is actually one of the two or three best sorcerers in the Marvel Universe as well. But he is not the Sorcerer Supreme. That is a title held by Dr. Strange. During the "Triumph and Torment" story, Doom and Strange did battle in a mystic arts tournament. Dr. Strange came out victorious, but Doom came in with a close second place. Coming in second gave Dr. Doom the right ask a favor that cannot be denied by the winner. Doom asked for the aid of Strange to help him free his mother from Mephisto's realm of Hell.
This movie would end up being more about Dr. Doom than Dr. Strange, but the idea of seeing a bunch of sorcerers in a contest is already pretty amazing, but then to see Doom and Strange doing battle in Hell itself is hands down worth the price of admission and then some. Dr. Strange may have a bunch of other villains like Dormammu, Shuma Gorath, and Baron Mordo, the "Triumph and Torment" story would be a great story to tell. Especially the ending. Sorry, no spoiler.
Avengers vs. X-Men
The question that is asked more times than we would all like to admit is who would win a fight between The X-Men and The Avengers. Does Logan fight with The X-Men who are his family, or does he fight for the Avengers because he feels that Cyclops is wrong? Are the X-Men's vast numbers too much for the Avengers, or is Captain America and Iron Man's planning too much for the Children of the Atom? In 2012, Marvel finally put out the crossover to answer that question (granted, the question wasn't really answered and they just fought). It started with Captain America going to the X-Men's home of Utopia and ordering Cyclops to give him Hope Summers (a young mutant) for the sake of the world. Cyclops did not like being told to give up one of his own people to Captain America who Cyclops called a "Fascist." All Hell broke loose after Cyclops hit Cap with an optic blast and Cap ordered the Avengers to attack.
Seriously, who doesn't want to see this fight? There are people who probably can't stand comic books and or comic book movies who would be intrigued to seeing this battle. Iron Man vs. Magneto (they ended up fighting in space), Red Hulk vs. Colossus, Luke Cage vs. Warpath and even if the story was changed and Wolverine sided with the X-Men, then you get Wolverine vs. Captain America. The story ended up lasting twelve issues and with the way the first half ended, it could easily be a two part movie. Closest we are going to get to that is probably whenever The Hulk fights one of the Avengers.