Excellent, people have started seeing Cap 2! I can finally post some thoughts on it (and really, really, REALLY massive spoilers will be here so don't read this until after you've seen the movie, I've refrained from posting until now to make sure not to give anything away and still don't want to ruin things for you!)

So, what we know about SHIELD now and how it relates to AoS: (Did I mention, SPOILERS!!!)
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So. SHIELD is basically in tatters. Rotten to the core with Hydra and ripped to shreds by the resultant battle. We now know Sitwell was Hydra. Agent Hand sent him to the ship on this weeks episode. It is therefore reasonable to assume that she, too, is Hydra. For Hand that's not a huge shock, but Sitwell? I frequently spoke on here about how much I loved seeing more of Sitwell and how he was Coulsons friend...I felt so angry and betrayed that he was dirty, my friends found it hilarious that despite that massive plot featuring major characters it was the betrayal by a minor character that I focussed on most!!

Nick Fury is believed dead by all but Agent Scherbatsky, random Doctor, Scarlett Widow, Cap and Falcon. I would guess that May has been reporting not to Fury but to Maria Hill on Furys orders. I think the tie-in may show Hill contacting May on the next episode while laying low with Fury and not knowing who to trust. It will be interesting to see whether they announce Fury as dead on the show, but there is just way too much that happens to Shield that I can't help but wonder how much of the film will be given away in the next episode if you haven't seen it.

Black Widow uploads SHIELDs secrets to the internet...it is implied by Pierce that this is a blanket upload of everything, even classified ops etc as he points out that all of the questionable things Black Widow has done will be public...if this includes EVERY secret SHIELD has then that has some pretty huge implications for the show...did they just publicly unveil the Index?! Is Skyes status as an 084 now known to everybody?! We know the exact nature of Coulsons revival was off book, but presumably his continued survival is, at least, a matter of record? Do the Avengers now know? (We learn that cap loves the internet, so I bet he reads up on everything that got posted!)

Lets go back to SHIELD being Hydra. My original theory, way back when the show began, was that Caterpillar was Hydra and that one of the team would be a traitor. My longstanding theory was Fitz = Hydra, as I figured one of FitzSimmons would be a bigger betrayal as they are inseparable and that Fitz was surprisingly competent in the field during the mission of the world most dangerous sandwich. If there is a Hydra mole on the team, though, I now don't know who it could be...looking at the team:

May - Implicated too much in the last episode otherwise I would have said her as the most trusted ally but now its TOO obvious. Also, she knows about TAHITI but we believe the clairvoyant doesn't. If she works for him, she would have told him, surely?!
Fitz and Ward - both sent on a suicide mission by Hand in the sandwich episode. If Hand is Hydra, why would she kill another hydra agent? That said, she may have known Ward was a survivor and he did just shoot fake-clairvoyant in cold blood. Because he was upset? Or because the Clairvoyant ordered him to tie up a lose end?
Skye - Knows about TAHITI, same as May
Jemma Simmons - If there is a hydra agent on the bus, Jemma seems most likely on the current basis - conspicuously absent when the kill order was made by Hand? Fits the Fitz theory above? Relentlessly trying to find out more about the miracle GH drug? I hope its not, as I love Simmons and don't want her written out, but she is now the most likely in my eyes.