1. What do the Space Marines do with Traitor Armor and Geneseed? I mean they can harvest geneseed and i assume they do, but in the case of the Sharks i'd imagine that gear is still GEAR.
Pretty sure they'd destroy it when it's logistically feasible to do so. They're certainly not going to use it for themselves, and leaving it laying around just gives other chaos marines a reason to raid you. So barring some sort of inquisitorial/mechanicus mission, I imagine they'd either leave it to rot or put a couple bolt rounds into it.
2.What is the difference in terms of quality between say Heresy Era armor (i think its MK3 or 4) and say Primaris Armor?
The protection offered seemly to be comparable. It's probably basically just upscaled firstborn armor with some plug-ins for Cawl's pet tech and default settings based on Cawl's preferences.
3. The Primaris Geneseed was a bit more stable and was said to have fixed some of the flaws, which flaws did it exactly fix?
Think this has been semi-retconned. When primaris were first introduced,
GW made it sound like primaris were free of gene flaws like the wulfen curse, the red thirst, etc. It is implied in newer fluff that nope, those flaws are still present, at least a little bit.
4. I've tried looking this up, but i've yet to get a concrete answer - Traitors scream "DEATH TO THE FALSE EMPEROR!"....who is the real Emperor then to them?
It's not necessarily that there's a true emprah, it's just that The Emperor is definitely illegitimate. Sort of like, "Not my president."
5. I've read a lot of the Death Guard and Smurf books and ....do you think they'll actually try to convert Mortarion? The Emperor seems to want, but i think GW is too far up their own ass and will just go "grimdark LOLS"? I think it would be kinda interesting to see a DG loyalist army and a DG traitor army on the tabletop - have Typhus just straight up replace Morty (nurgle likes him way more anyway and its all Typhus' fault)...I don't think this'll happen as Mort's already got a model n gak, but i think it would spin a neat narrative.
Eh... To each their own. Trying to "cleanse" Morty or some of his deathguard would be pretty awkward and out of tune with the rest of the setting. At the very least, plague marines (which I think basically all
DG are at this point?) are largely physically composed of semi-daemonic germs and logic-defying wounds. If you snap your fingers and make all the magic germs go away, you're left with a marine whose intestines are hanging out and whose other organs might be gone because they've been partially made of puss and tumors for the last few millennia.
As for Morty, I'm the first to say that
40k can get in its own way by doing the grim thing instead of the cool thing, but redeeming a daemon primarch seems pretty extreme. Like, if you can redeem a daemon primarch, then how irreversible is anyone else's chaos corruption really? And how hard do you make it to redeem him? Can the assassinorum start planning missions to redeem Fulgrim and Angron with warm hugs and therapy? It's one of those cans of worms that proooobably wouldn't be narratively interesting enough to be worth the downsides.
That said, loyalist vs chaos death guard can kind of be a thing. It's implied that some of the loyalist members of traitor legions got scooped up and quietly dumped into successor chapters after the Heresy, so you could totally have loyalist sons of Mortarion out there specializing in washing their filthy cousins from the galaxy.