Originally Posted by DrCosmic
It's more than just tying everything together it's "If Thanos doesn't get ended in Avengers 2 who are the Avengers going to defeat in Avengers 2?" Which, based on what we know about Trilogies and the clues Marvel has given about the culminations of Phase II and III coming from the build up of Phase II, it seems a very valid supposition.
And while Thanos may not work from behind the scenes anymore, he actually doesn't get his hands dirty until the climax, from what I've seen of him, as he runs a big giant empire. He fields others, both from his army and from Earth to do things for him as often as not.
The MoE, just happen to be the convenient thing for him to field vs more Chitauri or Ultron or Kang or any other Avengers villain. Would his goals overshadow those of the MoE? Absolutely. I think that's acceptable, because the MoE still carries the personal motivation angle, while Thanos is a relatively indifferent philosophical enemy. I think that works at least as well as the MoE being both the personal and philosophical enemies. Plus, it's not like the "real" MoE can't be done with Zemo later.
This is all based on the assumption that Thanos will be in the films past 2. I don't see any reason to assume that. Trilogies do tend to have one story that ties all three films together, but the character of Thanos doesn't have to be that binding element. The movie seemed to be a lot more about the Avengers themselves than the threat they faced. I see no reason to drag out Thanos' story beyond the second film.