Here is a continuation of my own list for my fan-made Marvel Universe this time with Phase Two.
1. Ant-Man: The Revenge of Ultron
I wouldn't have minded the change they made in Age of Ultron where Tony Stark creates Ultron instead of Hank Pym if it created an interesting character arc for Tony, but it really didn't. In this Marvel universe, I hand the keys to Ultron back over to Hank, after all he was the original creator in the comics. Included in this story would be the Wasp and the Vision because you just have to have them. Here, Hank creates Ultron in the hopes that it can prevent large-scale attacks on humanity so that there would be no need for the Avengers. It becomes a failed attempt to take the spotlight from Earth's Mightiest Heroes.
2. The Wasp: Civil War
Yes, if you can believe it, I would actually do the Civil War storyline that we're getting in the next Captain America film in 2016 and do it from the Wasp's point of view. There's nothing wrong with having a little bit of girl power every once in a while, and the Wasp in the Civil War storyline, in the comics anyway, is great. Included in this story would be Iron Man, Captain America, Ant-Man, and there would even be "cameos" of Wolverine and Magneto for reasons I will explain later.
3. Weapon X: The Origin Of The Wolverine
This story would jump back a few decades to give a new twist on Wolverine's origin. Don't worry, the story won't resemble X-Men Origins: Wolverine very much at all. This retelling of Wolverine's origin would bring in the Winter Soldier and Deadpool (our red-clothed buddy, not the mouthless all-powerful dude), with a few flashes of Jean Grey, and it would show how certain events actually plant the seeds for the modern and present worldview on mutants and how it paves the way for the huge battle that's coming...
4. Deadpool: The Merc with a Mouth
Every version of the Marvel Universe can use a Deadpool every now and then, and this would be the time. With Wolverine, and even Daredevil involved (because it just made sense), Deadpool would get a story of his own here, and it all leads up to...
5. The Avengers vs. The X-Men
This is the "huge battle" I was referring to earlier. This is something that for the time being MCU fans can only imagine. With the repercussions of Ultron's actions and the aftermath of the Civil War, it all comes down to an immense battle between the Avengers and the X-Men. Imagine how the Avengers are celebrated and praised as heroes by the public while the X-Men are feared and chased away by the public because their powers are viewed as a result of something being "wrong" with them. Also, consider that Captain America's and Wolverine's teamwork together in Shadows of the Past from my Phase One would be brought up again here and gives the story some added drama because now they are actually fighting. Also consider the fact that Professor X served as somewhat of a therapist for Bruce Banner and Donald Blake in the first Phase and they are also fighting each other now.
So what do you guys think of this phase? Sound off in the comments below! I can always make changes if you guys really think I should make some.