My favourite part of the inter connectivity between the movies in Phase 1 was how the Tesseract was used. An Asgardian artefact uncovered and used by the Red Skull and HYDRA and then kept by SHIELD until present day? That's awesome.
What do you think it'll be in Phase 2? I think Iron Man 3 and Cap 2 will be connected in a few ways, and MAYBE Ant-Man if it's set in modern day rather than the 60's. If it is modern day, then I expect Radioactive Man to be the villain, following from IM3.
If it's set in the 60's, then I think it would be cool to have an Infinity Gem - preferably the Time Gem - to be the MacGuffin of Phase 2. This will be the thing 'everybody wants' that the GOTG have in their movie, and there will probably be some sort of hint in Thor: TDW that it's around and Thanos is after it.
To stop Thanos getting the Gem, the Guardians will send it back in time to Earth in the 60's where it falls into the hands of Hank Pym and SHIELD. Upon testing on it, it teleports Pym and Janet into present day, but the Gem is still stuck in the past.
It would allow for another period MCU movie, and could feature appearances from Howard Stark, Nick Fury and show the formation of SHIELD.
Plus then in A2 he and Cap could become buddies as they're both men out of time.
Maybe since Wang Xiuxi (however you spell it) is in his 60's/70's in IM3 we'll see a younger version of him in Ant-Man, where he is Radioactive Man and is cured by the end?
I literally came up with this 5 minutes ago.