I still maintain that the Time Gem is going to be part of Thor: Ragnarok. Ragnarok is a cycle in the comics which Odin prevents through the use of time travel. (Hence why in the Eddas, Thor was a redhead, Sif was blonde and Heimdall was fairest of the gods.)
The Time Gem needs to be present to save the universe from Surtur and keep Ragnarok as a reset button.
The Soul Gem is either going to be the Eye of Agamotto in Doctor Strange or it's going to be part of Guardians of the Galaxy 2.
Considering that Guardians 2 pretty much needs to establish Adam Warlock for Infinity War and he has the Soul Gem in the comics, that's the more likely option. In which case, the plot is presumably going to be based on the Abnett/Lanning run where the Matriarch and Universal Church of Truth were the main antagonists. The Universal Church of Truth worship the Magus who is Adam Warlock's evil counterpart and will presumably be the villain in Infinity War: Part 2. My guess is that the plot of Guardians 2 is going to revolve around Adam Warlock being mistaken for the Magus and worshiped as their god against his will.