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This is an idea I've had floating about for some time, based on redoing the 4th ed Chapter system so it isn't as "min-max" (Taking pointless "disadvantages" for meaningful advantages, etc), as well as taking some ideas from Deathwatch: Rites of Battle. Some "Create a religion" from Gods & Kings is there too. The main thing is fleshing out the system, trait suggestions, etc.

There are several different types of Chapter Traits available.

Codex Deviations: These are either major or minor; whether it's having Chaplain/Librarians (Silver Skull Prognosticators), or Apothecary Sergeants (Iron Snakes, Red Scorpions, etc), or radical reorganization of your chapter. Honor Guards, or veterans of Tyrannic Wars are acceptable within codex regulations.

Geneseed Mutations: These could be anything from bestial aspects (Space Wolf Canis Helix, Bone Dragon exoskeletons, etc), Psyker-attunement (Blood Ravens), Heavy-G worlders (tougher/slower/etc), or not having Gulliman as your spiritual liege.

Chapter Secrets: Has a sizeable portion of your Chapter fallen to Chaos (Dark Angels/Blood Ravens), possess and exorcise Daemons among their initiates (Exorcists), use Chaos Artifacts against their owners (Blood Ravens, Relictors), make use of non-sanctioned Xenotech (Mentors, Silver Sharks, etc), or otherwise have skeletons in their closet they would not reveal? Are they circumventing Chapter size (Black Templar)? Note that this represents Chapter-wide corruption; obviously the Ultramarines would *never* resort to consorting with Xenos, using Chaos artifacts, Xenotech, or anything heretical, and don't let the Eldar, Tau, Marneus Calgar, or Uriel Ventris tell you otherwise! Why, those Eldar are just jealous that Calgar's gloves fisted their Avatar, and so they must have gone about spreading that rumor his Gauntlets of Ultramar belonged to a Chaos Warlord...don't pay them any heed. The Gauntlets of Ultramar are from Ultramar. It's even in their name!

Renowned Aspects: These traits represent the chapter having an established reputation for being the best, an example by which other Chapters aspire to. Whether Scions of Mars (Iron Hands), they are masters of Combat Tactics, etc.

So how do we go about creating a Chapter? Simple.
-Select a Major Codex Deviation, two Minor Codex Deviations, or a Renowned Aspect.
-Select a Major Codex Deviation, two Minor Codex Deviations, or a Renowned Aspect.
-Select a Geneseed Mutation, or a Renowned Aspect.
-Select a Chapter Secret, or a Renowned Aspect.
-Select a Major Codex Deviation, two Minor Codex Deviations, a Geneseed Mutation, a Chapter Secret, or a Renowned Aspect.

Basically, you can take a lot of Renowned Aspects if you want your chapter to make Gulliman proud, *or* you can make a loyalist Chapter that is borderline-heretical/an unfortunate result of the Cursed Founding, or anything in between with a sliding spectrum.

Minor Deviations
-Armored Behemoths: Cannot take Land Raiders, except as Dedicated Transports. (Aurora Marines, Blood Angels, potentially Black Templars).
-Dual Responsibility[X,Y]: Select two HQ roles; you cannot take them separately anymore, but can take an HQ with both. (Examples: Space Wolf Wolf Priests are Chaplain Apothecaries, Iron Hand Iron Fathers are Chaplain Techmarines, Silver Skull Prognosticators are Chaplain Librarians).
-Street Sweepers: Tacticals cannot carry a Heavy Weapon, but can take a second Special.

Need more Minor Deviations in general.

Major Deviations
-Specialist Sergeants[X]: Select a particular Specialist Type. You may not take Specialists of this type as solos anymore, but instead, all Tactical Sergeants must be replaced by this type at the appropriate points-cost. (Example: Iron Snakes w/ Apothecary Sergeants).
-Trial By Fire: This army does not have separate Scout Squadrons, but may include Scouts in their Tactical Squads.
-Exalted Role [Unit Type]: Select: Bikers/Terminators/Assault Marines. These can be taken as Troops; the unit type can be taken in its normal slot at +10 points/model for +1 WS/BS/W/A. (Or something along those lines/bears tweaking).

Mutations
-Battle Trance: (Working this one out. Think Mantis Warriors. Extra init, or battle focus ala Eldar? )
-Beastmark: (Some version of melee rending?)
-Blood Rage:
-Overdeveloped Organ (Ossomodula, Betcher's Gland, Cataplesean Node, etc)
-Psychic Boon: (Basically, 50 points/squad for psyker sergeants. Think Grey Knights or Exorcists).

Chapter Secret:
-Above Regulation: Choose a troop choice. The maximum squad size of this unit is increazed by 5.
-Inner Circle: (See: Dark Angels)
-Proscribed Artifacts (Daemontech, Xenotech...Heretek?): The specifics of this one are still being worked out.

Renowned Aspect:
Abhor the Witch, Destroy the Witch: Adamantium Will and +2 WC during the enemy psyker phase, cannot take Psykers. Cannot be taken w/ Psychic Boon.
Bolter Drill: See 6e Imperial Fists.
Aspire to Glory[X]: Think the assorted Space Wolf Sagas from 5e, with the "deed"/requirement of them being a tactical objective.
Cleanse and Purge: Twin-linked flamers/meltaguns
Combat Tactics: See 6e Ultramarines

Scions of Mars: Master-Crafted Plasma.
See But Remain Unseen: Stealth. Mutually exclusive w/ Take Pride in your Colors.
Take Pride in your Colors: Standards/Banners with a bubble effect have +6" to their radius.