Re: Who should be the villain in an Avengers sequel? (Poll)
Anyway, Joss hints toward Thanos in Phase 3? I'll run with it. He's also mentioned "villains" plural.
I assume some combination of Ultron and/or the MoE for Phase 2. Also, if he insists on using Quicksilver and Scarlet Witch they will indeed likely start out as MoE.