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So seeing the leaks for the HH starter box and having a desire to play non primaris marines, I have been thinking of trick...convincing some of my friends to play prohammer or HH. My lgs has a box of Mk 3 marines. Do these get used a lot? Does it depend on the legion or is it all just flavor?

Every Legion used every armour from 2-6 throughout the Heresy and there is no rules difference between them.
However if you like theme's in your army then here's some background tidbits:
Mk2 - The first pattern of armour used by the Legions. Started to get rare just before the Heresy since it was showing its age. Still favoured by the Iron Hands, Iron Warriors, Salamanders and Death Guard.
Mk3 - An improvement on Mk2 with a focus on defence and Void warfare. Very common amongst all the Legions.
Mk4 - A flat improvement with slightly less defence than Mk3 but with better integrated systems and was generally more advanced. The first Legions to join Horus received a huge number of these suits from the Mechanicum as gifts.
Mk5 - Mk5 started off as prototypes and cobbled together armour taken from many different sources. Very much a case of "use what we have" and would not be uncommon in the Shattered Legions (Iron Hands, Raven Guard, Salamanders).
Mk6 - This was designed for aerial assaults by Corax with the Raven Guard and somehow the Alpha Legion getting the bulk of the prototype and early production suits. By the Siege of Terra both sides had distributed the design across their forces.
Mk7 - This was the "apex" armour for the Legions but was only in the early prototype stage as the Heresy started and an extremely limited amount of suits were evacuated from Mars and given to the Legions defending Terra (Imperial Fists, Blood Angels, White Scars).
Mk8 - Specifically a post-Heresy design but could be used to denote Artificer Armour on a Sergeant.

Excellent! Thank you.