We finally got some confirmation of the intentions of the Emperor regarding Space Marines and humanity.
Malcador said that transhumans will never rule mankind and that this is the command of the Emperor.
Guy Haley said that Roboute is going against the Emperor's wishes of having humans rule rather than Space Marines.

Why was the Emperor so adamant about humans ruling when Space Marines are superior in every way?
The Era of Ruin even suggests that the Emperor was going to Thunder Warrior the Space Marines.

This is really bad for the loyalists because all of this affirms the position of traitors like Abaddon. Abaddon was right about the Emperor denying the Space Marines their right to rule what they bled to build. The Space Marines were betrayed by the Emperor. The rebellion was honest and just after all.