The only real concern would be the questions of why didn't Lumley etc realise he was still alive. Hmm, I wonder how much info on Skye his security clearance has granted him, he wouldn't know she was an 0-8-4 from reading files but would he be able to find out that SHIELD had something to do with her foster care. She never went through any sort of entry tests etc so there is possibly not too much information on her as an adult in their system to begin with.
Do we think his interest in the GH325 is about this "Phase 3" aspect of Centipede, or more to do with personal injuries. I'm somewhat curious as to who knows about his metal plate, and to what extent has he been "enhanced" (somewhat similar to Deathlok tbh, what was the reason they put a plate under his skin etc). Many many questions still to be answered, not all important to the story, but still interesting to know. Another one is was Akela Amador being controlled by Centipede too or someone else who had access to the tech, which I assume was made by Cybertek.
The 'Its all connected' thing is pretty huge, in the first few episodes there are (off the top of my head):
- "This is an origin story" Mike Peterson
- "An object of unknown origin, kind of like you" Coulson to Skye
- "Best espionage marks since Romanov" about Ward
There's also a point where May/Coulson say "we agreed to protect her from the truth", before they find out she's an 0-8-4, and back when May was still cold on Skye... so they at least knew something about her.