I think the issue is that some of the cults don't have good representation outside of the troops slot. Specifically 1k Sons and Noise Marines. Noise weapons for anything with a Slaanesh mark and all units in the army being either Slaanesh or unmarked would have been nice. Something similar involving sorcerer covens for Elite and/or HS and Rubric Termis would have been nice too.
For the legions HQ choices like this would be nice:
Iron Warriors - Cover save debuff, something like the Master of Ordinance though, not the Techmarine stuff that the current Warpsmith gets.
Alpha Legion - Cell Leader: Cultists get better gear, maybe some infiltrate mojo and redeploy shenanigans like Lady Malys?
Word Bearers - Dark Apostle: Cultists are Fearless, leadership buff for you and leadership debuff for enemy?
Night Lords - Fear, lots of Fear, and leadership debuffs. And can see in the dark too.
And the above choices would be exclusive, so if you choose a legion HQ, no picking a second HQ from that list for mix and match. I dunno, the CSM codex is what it is, and it's going to be that way for years to come, so I guess I'll just have to deal. I just don't like that the cults feel incomplete, the HQs seem like very 'rough' matches for some legion traits, and there's a whole lot of 'counts-as' involving the marks for them to work out for all units (Slaaneshi Oblits taking the MoN which is counting-as Combat Drugs). I mean it works, but it doesn't work smoothly and involves paying no attention to the man behind the curtain, which makes me a sad panda.