I Think he did care about the Primarchs, they are after all the only beings that he could sort of empathise with, they are also the fruit of a substantial amount of effort and planning on his part and pivotal to the success of his plans.
i would however add that really the Heresy itself, the betrayal of Horus was really, in the grand scheme of things just a minor setback, the only true blow (other than making the Emperor into a vegetable) was the irreparable damage Magnus did to the webway, its because of that the Emperor couldn't leave the Golden throne, its because of that the majority of his psychic power was tied up with the webway, making unable to fight the traitors directly, and if the webway worked, the imperium could have healed, the traitor forces routed and mankind enter into a new prosperous age.
so in a way, even if he didnt care about some of his sons, it was largely inconsequential, the only true blow was that of Magnus, born out of his arrogance and pride.
And the fact the Emperor showed some of his sons paternal love dosent mean they would turn out the way he wanted, he loved Horus and how did that turn out? he Fulgrim his own persoanl symbol to wear and look at Fulgrim now, so really, being more loving/helpful dosent ensure loyalty.
And as for Malcador, i believe the strong bond comes from the fact they are both immensely powerful psykers, probably friends before the primarchs were made, they shared the same goals and ideas, they trusted each other and the Emperor even possessed him a few times, but he definitely at least liked some of his sons he acts like a father to dorn and from the fluff i read he seemed to like Sanguinius quite a lot, he also seemed to hate Russ when they first met, but they eventually came to love each other.
Futhermore, on the subject of lorgar:
+Word Bearers, hear me well. You, among all my Legions, are
guilty of failure. You number more warriors than any other, excepting
the XIII. Yet your conquests are the slowest, and your
victories ring hollow+
+You linger on compliant worlds for years after final victory,
driving the populace into the worship of false faith, seeding cults
of the naive and the deceived, erecting monuments to lies. All
you have done in the Great Crusade is for naught. While all others
succeed and bring prosperity to the Imperium, you alone
have failed me+
the Emperor has seen, countless times the deteriorating effect of religion and how it can be manipulated by chaos, the Emperor gives Lorgar a purpose, a reason, an objective and Lorgar not only turns the reasons on its head, he also does a crap job of it.
The Emperor didnt mind the wolves being somewhat excessively (in certain ways religious) or the Martians worshipping him, or the use of psychic powers in the thousand sons,or the crazed lunatics in the world eaters and night lords, mutations of the blood angels, but because they achieved their designated purpose he overlooked it, they were flawed but they got the job done, Lorgar was flawed and did fuck all.
Last edited by Lost&Damned; 07-13-12 at 01:39 PM.