Well this book has given us quite a bit to talk about now hasn't it. Lets start with what i see as the big stuff:

1)The traitor legions have access to the webway ( tho i think they might just never mention this again).
2)The Emperor did not really care that much about the Primarchs, seeing them ultimately as tools and not sons.
3) The Emperor has no idea what to do once the webway project goes south.
4) The Emperor could have killed the Primarchs rather then let chaos take them.

Also things i am not 100%, if when the webportal to Terra reverts to stone the Emperor can go soul search in ruins does this mean he doesnt actually need to constantly be on the throne? Even if he does, why dont they just hook up more psykers during the siege? Why does Malcaldor need to die?