**WARNING: CRACK THEORY AHEAD**
I've been thinking for awhile that The Primarchs are (for lack of a better example and you'll have to suck it up if you don't read Rowling) The Emperor's horcruxes.
In general-he tore off parts of his own soul to form the souls of the Primarchs, which explains why they all have some aspects of his personality (Horus the leader, Magnus the Psyker, etc) and also why the Emperor is in his current condition (parts of his soul have been corrupted by chaos-namely those primarchs that are now Deamon Princes.)
Anyway, that's a theory that's probably the result of SOMEONE HERE watching the movies too much but sort of works with the given data.