OK, I've just caught up with the last couple of episodes. Can't wait until Season 2!
A few thoughts:
Loved Garrett's final appearance and his big bad speech and then Coulson vaporising him. Very Joss Whedon - remember Dracula and Buffy? "You think I don't watch your movies? You always come back."
Wondering (because I still have a bit of a crush - there's no hope for me) what they can possibly do with Ward's story arc now. Particularly after what can only be interpreted as his threat to rape Skye in their final confrontation. Surely there can be no redemption story for him now - but then again, this is Joss, and look at Spike (who did a lot more than threaten). I would be sad not to see Ward back next season.
Loved the reappearance of Fury - how cool is Samuel L. Jackson?! Hanging out of the helicopter in his shades and great hat 
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This is a really interesting review of Ward's character arc, by the way.
Reading some of the fan forums, etc, I think there's a lot of Marvel Universe creeping in though, especially with the blue alien that's the source of Coulson's cure and the diagrams that he and Garrett were drawing. I wonder how much we need to know/watch to be able to truly keep up and get all the references?
Can't believe the DVDs aren't out until September! What's that all about?!
Hope someone's still out there to talk to about this - sorry to take so long to catch up with it all...
Still traumatised by the death of the dog 