The Tesseract is indeed the Power Stone, as it's been mentioned numerous times to have limitless power.
The Stone in Loki's Sceptar/Staff is the Mind Stone, confirmed everywhere.
The Aether is undoubtedly the Reality Stone, as Jane Foster says something to the affect that " the fabric of reality being torn apart."
The stone featured in GotG, will probably be the Space Stone.
That all being said, that leaves us with 2 remaining stones.
I agree with the theory that the Eye of Amagotto will be a stone, almost certainly the Soul Stone.
NOW, for the crazy theory involving the final stone. the Time Stone will be introduced in the Age of Ultron..How? By having Scarlet Witch find the Time Stone, somewhere on Earth, which they use to take a note from the AoU Comic & kill Ultrons creator, Tony Stark. Go back in time to the surgery to remove his Arc Reactor in China, have some complications, BAM, gone.. This will explain the absence of Tony in phase 3, & possibly beyond. Once all the Stones are reunited, or at least the Reality Stone, to bring Tony back for the third Avengers film.