1) Coulson is Not A Robot
Seeing Coulson first get stabbed through the chest and heart by Loki's blade, then seeing his human-looking brain get operated on, confirms that Coulson was not and is not a Life Model Decoy, nor is he the android Avenger known as Vision - a common fan theory immediately following the events of The Avengers. That doesn't mean he can't become Vision one day, especially with all the upcoming connections, from Scarlet Witch to Ultron, but he's not right now.
And that doesn't mean The Clairvoyant, who can seemingly kill people via smartphone, isn't connected to Ultron. After all, we're told Ultron is a threat The Avengers see coming, hinting at an introduction or at least some teases in the films before it (see: Captain America: The Winter Soldier - which just so happens to premiere around when season one of Agents of SHIELD concludes).
Coulson is not a mechanical man nor do we believe he's a clone. It's bigger than that.
2) Asgardian Magic
The references to "The Magical Place," the still-mysterious operations Coulson went through, and the interesting word choice at the end of the episode when Coulson is told that Nick Fury moved "Heaven and Earth" to make sure he lived, all tease a potential connection to Asgard. Heaven & Earth is actually the title of a Thor comic series.
Coulson being an Asgardian or healed by Asgardian "magic" (after being killed by a half-Asgardian) doesn't quite fit though - especially seeing the amount of death in Thor: The Dark World where soldiers dropped like flies - not to mention Thor's mom, Frigga, getting stabbed and being killed off. Coulson being of Asgardian descent would be lazy storytelling, considering his encounters with Thor and another Asgardian in Episode 8: The Well. Don't count on it.
Page 3: The Inhumans & Kree Connection
Agents of S.H.I.E.L.D., starring Clark Gregg, Ming-Na Wen, Brett Dalton, Chloe Bennet, Iain De Caestecker and Elizabeth Henstridge, returns next Tuesday with “Seeds” @8pm on ABC.
Captain America: The Winter Soldier hits theaters April 4, 2014, Guardians of the Galaxy on August 1, 2014, The Avengers: Age of Ultron on May 1, 2015, Ant-Man on July 31, 2015, with unannounced films coming May 6 2016, July 8 2016 and May 5 2017.
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