Aside from all the other things y'all have pointed out, the one thing that really stuck out at our AoS watch party (we all saw CA:WS over the weekend to prep ourselves) was the implication that Coulson was working for Hydra up through his death...
A theory one of our group tossed out is that Fury was beginning to discover the conspiracy and took the opportunity to use Colson - once resurrected (either as a LMD or real resuscitation) - as an agent outside of Hydra's influence.
Regardless, we're all hooked once again on this, and we're starting a rewatch from the beginning to see if we can spot other Hydra-signs.