Honestly, I haven't seen Iron Man 3 yet, and I understood the Extremis thing fine.
Same here.
I liked it. It felt like they were setting up plenty of different things and I look forward to seeing it all play out.
This may sound odd, but I was certain that Coulson would be killed in this episode (or only be in flashbacks or some other thing that would have stopped him from being in the rest of the series). I really thought the huge promotion involving the character and actor was a huge Whedon-esque misdirection but I'm glad I was wrong.