Currently, this is my idea of how the chapter creation system will work:

The Easy stuff:

Chapter Name: (derp)
Chapter Colours: (Describe, or post a picture of, the what Average Joe Astartes looks like)
Chapter Master name:
Founding: (When was your Chapter founded?)

The stuff that makes actual variables to your stats:

Descendant of: (Which Legion do they use the Geneseed of? If you want to use a traitor legions gene, then be forewarned, this will grant no bonus', but, naturally, a number of penelties. That's not me being a dick, it's how the universe works. You want to be descended from the Iron Warriors, that's your choice, just know that if the inquisition find out, there's a 90% chance they are gonna call Excommunicate Traitoris. There's also a higher likelyhood of a bad mutation happening.)
Closeness to Civilians: (Every Space Marine Chapter is charged with protecting civillians, if your chapter is close to civillians, then your resource gathering/recruitment is increased, but be warned, the closer you are to them, the more they can effect you with negative influence. you have 3 levels: "We are as one" your Space Marines live and work with the populace during their down time, they take brides and raise children, every civilian dreams of becoming a Space Marine, but every negative influence takes it's full wrath upon your chapter. "We protect our charge" The Civilians see you as their protectors, though most will see one in their life, they will live content in the knowledge that the emperors finest are watching over them. any negative influence on them marginally affects your chapter "We are as gods to them" Civilians NEVER see one of your chapter, until they are called upon to join, the average civilian doesn't even believe that the Astartes even exist, to them, they are just a myth, a story to keep children from being afraid of the Xenos. The thought of joining the Space Marines is just a childish fantasy. You care not for them, and they care not for you, whatever happens to them is none of your concern.)

Stuff that is decided by dice roll:

Gene Mutation:

Chapter Strength:
50 points to distribute

Battleforce = 10 points (A Battleforce counts as exactly 100 battle points.)
Battlefleet = 10 points (A Battlefleet counts as exactly 100 battle points.)

Upgrades: (Each upgrade grants extra Battle Points to the force they are on.)

Kraken Rounds = 2 points (+5 battle points, limited to 1)
Refined Promethium Fuel = 5 points (+5 battle points, +15 battle points in Fast Attack Missions, limited to 1)
Tech-Marine = 3 points (+5 Battle points, +10 if Titan is in Battleforce. No limit)
Knight Titan = 10 points (+20 Battle points*, Limited to 5)
Veteran Commander = 5 points (+10 battle points)
Relic = 10 points (Roll on the Relic's table to see what they get and it's bonus'. A battlegroup may only have 1 Relic. I'm making the Relic table at the moment, it could be anything from a Primarchs weapon to an Emperor-class Titan. Just know that it's a gamble, some things will be absolutely amazing, whereas other things will be... Not so amazing.)

Turn Order:

We each take turns, naturally. Each turns counts as a year for our chapter. First things first, calculate your income based off of how many worlds your chapter controls, how many battles you are currently in and any other modifiers. Then, you roll on the Happenings table, which is a d20 and a d10, which will determine what happens this year to your chapter (Meaning up to 200 different things could happen to you) it could be anything that a Chapter might face. I'm currently deciding what these things could be, but input on them would be greatly appreciated.

You can always:
A) Launch an invasion (Invade one random planet with one battlegroup of your choice. If successful, you can bring that planet under your control. Its stats are randomized.)
B) Launch a Crusade (takes 5 turns. you dedicate as many battlegroups to it as you like, you may also ask for assistance from other players, asking them to send you a battlegroup to help. Reaps big rewards if successful.)
C) Gift Relics (If you have a Relic that you do not like or do not need. You may trade it for something that another player has. Or, gift it to the Inquisition. This relic is perminantly removed from the game. Each Relic gifted to the Inquisition increases your chances of passing their next inspection.)

Characters:

Characters sound somewhat confusing, but are pretty simple. To get a character, you just need to pay 3 points... That's all. He starts as level 1, and is then attached to a Battleforce and is worth 5 BP to them. Every event that he is a part of, good or bad, win or lose, he gains 1 experience point. His level increases whenever he has experience points equal to his level (E.G. he needs 1 XP to go from level 1 to level 2 and 2 XP needed to go from level 2 to level 3.) XP of course resets after they go up a level. Every level gained adds +5 to his base bonus'.

Specializing:

Once a Character has reached level 3, he can begin to specialize, different specialities grant him different bonus:

Tactical: (+5 Battle Points)
Devastator: (+10 Battle Points, Cannot be brought on Fast Attack Missions)
Assault: (+10 battle points during Fast Attack Missions)

Then, at level 5, you can upgrade them to an Individual Character. If you do this, then you choose what kind of character they are upgraded into:

1) Chaplin
2) Librarian
3) Apothecary
4) Techmarine
5) Sternguard

Death of a Character:

Whenever a Battleforce suffers critical losses, you may roll a die to see if your character makes it out in one piece. If so, then he is perfectly fine. If not, then don't worry about him, the first time, as he will be given Cybornetic enhancements (+2 Battle Points) and sent back to combat after your next turn. If he dies again, then you need to make a +4 save. If failed, then he is dead, but if he makes it, then he is, again, absent for a turn, but instead of getting Cybornetic enhancements, he comes back as a Dreadnought. (Loses his Speciality and instead gains +10 Battle Points, cannot be used in a Fast Attack Mission) Unfortunately, this means that he Cannot serve as a Commanding Officer of the Chapter, he cannot be elected as one, and if he is already a part, must step down, due to the mental degradation that Dreadnoughts Suffer from.

Commanding Officers:

Commanding Officers are a promotion for a character, only certain Individual Characters can take certain positions, and a position can only be filled once.

Chapter Master: (Automatically receive one to begin with. Required to perform actions.)
Master of Sanctities (Chaplins Only: Lower the effect of negative Civilian effects to the rank lower.)
Chief Librarian (Librarians Only: May Reroll on the Relics chart once per buy.)
Master of the Forge (Techmarines Only: Reduce all buying costs by 1 (To a minimum cost of 1))
Master of the Apothecarion (When taking a critical loss, make a 3+ save, if successful, then it is downgraded to a loss)