I'm intrigued by the Talosians idea. Harrison could be a Talosian or be representing them -- An altered human or perception altered Talosian doing their bidding for some Talosian plot. We know that they can cure physical deformities, which is a theme explored in the film trailers. The "behind glass" imagery is conversely reminiscent with scenes from that pilot episode. A Captain Pike connection. Even a screaming Alice Eve fits the bill, is she being mind tortured similarly as they did Vina?
In the Cage, their Talosian planet is in ruins, do they blame Starfleet? Humanity? Or just all other space faring lifeforms... what would you do for family?
They can alter perceptions, and enjoy pitting us "lesser lifeforms" against each other, pushing emotional buttons to reveal humanities true nature. Causing a inner Starfleet conflict would be right up their alley. Maybe Kirk possibly breaking the prime directive brings attention, and perhaps, inspires the powerful Talosians to test the Earth men's hubris as we boldly go further into space. This would be a fabulous concept, to explore Trek's very first adversaries.
I hope it's this.