I'm not sold on the Primarch as a character upgrade actually.
ATM if you put the Primarch with anything other than something with RA it's just too weak. There's nothing worse than the focus of an army being mowed down by game mechanics (i.e. surrounded and engaged to death by assault marines)... I know Titans can be downed in much the same way but a Primarch should be bloody hard to kill. Brainstorm:
if you do manage to kill one, perhaps make it a game objective for capture; or all friendly formations gain a BM upon his death???
Given they are essentially "demi-gods" I think perhaps just make it a WE (like the Avatar with COTYK). In the end the troops around the Primarch become "superfluous" to the drama of a Primarch and abstraction means the loss of the troops around him has little overall effect on the unit.
If folks prefer to have a specific Primarch with a specific unit type a special rule to add the abilities of that unit to the WE might work. e.g Jahagatai Kahn could be given an Honour Guard of bikes which would in turn grant the WE mounted
or Alpharius might get scout
if attached to a Reconnaisance unit and so on....
Lastly, I think if you're going to include Primarchs they should really be fleshed out individually for abilities. Epic is usually abstract for character types but in this case I think they're a special case.
Anyway, just some ideas.