The OP specifically asks "If Whedon decides to go MoE this time around..."
The theory going around now, I believe, is that Thanos will stretch into Phase III, thus, some additional villains will be in Avengers 2 to be defeated since Thanos won't. The MoE seem likely choices.
More than the lineup, I'd love to see Thanos actually assembling these people Fury style. It'd be crazy.
Originally Posted by jaqua99
a variation of these guys.
This seems most right. I don't think we'll get Masterminds like Madarain and Malkeith in there, though. I suspect they'll go Red Skull before trying to introduce Zemo, though Zemo is pretty great.