I very much think we will see the MoE. As CosmicCap said, CA:TWS will play the biggest role in setting up AoU. I can't believe this would mean anything other than setting up the Masters (of Evil) as The Avengers greatest perceived upcoming threat. And the reason they develop Ultron to begin with.
I think Ultron would be needed to break the Masters of Evil out of SH.I.E.L.D. custody. I think this is the kind of storyline the movie will follow:
-Tony creates Ultron, who is the next big thing for Tony. Kind of like creating the Mark 2 and 3.
-Ultron's A.I. is corrupted and JARVIS is infected.
-Ultron, knowing every dirty secret S.H.I.E.L.D. has ever tried to keep, heads to the Triskelion.
-Captain America is at the Triskelion following the events of Captain America: The Winter Soldier.
-Ultron, knowing that Captain America is an Avenger because of JARVIS, combats him. Unsuccessful, he flees with the freed Super Villains.
-Ultron, assembles them in order to distract the Avengers so he can plot the perfect trap.
-The Avengers and Masters of Evil battle and the Avengers win.
-Ultron creates Vision, I'm not sure how yet, and Vision takes the Avengers to Wakanda.
-Ultron has a new body made out of Vibranium and is ready to take on the heroes.
-The Avengers defeat Ultron and Iron Man realizes he is actually needed to pilot the suits.
Some outliers in this story:
-How will Quicksilver and Scarlet Witch be involved?
-If a final battle takes place in Wakanda will Black Panther be involved?
-How will the Avengers actually assemble?
-Could Ultron possibly create Ragnorak?
-Will Ultron use an army? Would they be Iron Man suits or generic robots, etc.
-Will Iron Man create a new suit to fight Ultron? If so, which one? Finished Extremis, Bleeding Edge, Godkiller, Black and Gold, etc.
-How will everyone perceive Tony after this?
-How is Vision created and will he have a love interest with Scarlet Witch? Will Hawkeye be involved?
-Who will make up the Masters of Evil?
-Lastly, how or who actually creates Ultron? SH.I.E.L.D.? Tony? Or is it a combination of events? A combination of ideas or people?