ARGH I keep losing my posts.
Look, I didn't say that SoB's were Female Space Marines- I was suggesting to the vast majority of outsiders that they would APPEAR to be, and that to satisfy the niche a female space marine would fill one should just USE the SoB's. A female space marine is just silly and would frankly be fugly, and would also not be accepted by the imperial faction and is thus unfit for a player character.
You have to simplify things, if you saturate it with too much fan stuff and too much fan customization you dilute the message and theme of the story. Alternative space marine chapters with different stats would be too much- as would different eldar craft worlds or chaos gods. K*I*S*S. Otherwise it frankly, smacks too much of fanservice or worse, fan fiction.
Moreover, there needs to be cohesive 'sides' to the war. This is not to say having every faction fight each other is a bad idea, but there also should be an option for on the fly alliances. To simplify things the Imperials should be boiled down into ONE faction- the Imperials.
The Imperials would have Space Marine, Imperial Guard, Inquisitor, and Sister of Battle as classes.
The Eldar could have the Wailing Banshee, Warlock, Warp Spider, and Striking Scorpion classes.
The Tau could have the Kroot Warrior, Fire Warrior, Kroot Shaper, and Pathfinder classes.
Chaos could have the Chaos Space Marine, Sorcerer, Heretic, and Traitor Guardsman classes.
Da Orkz culd have da Slugga Boyz, Shoota Boyz, Wierd Boyz, an da Pain Boyz classes
The Dark Eldar could have the Warrior, Haemonculus, Wych, and Mandrake classes.
To supply the level of customization and the many unique units not given their own class, a "merit" system very similar to Fallout's 'perks' could be implimented. Every 10 levels or so you take a Merit which gives you status effects, new abilities, equipment, or equipment options. Ex- to play a Commissar your Imperial Guard character could take the "Indomitable Will" merit which supplies you with an aura that increases allies resistances and weakens enemies, the "dual wielder" merit which allows you to dualwield melee or ranged weapons OR combi wield a sword and a pistol, and the "Fencer" merit which increases your attack and parry/block speed and ratings in melee. To make a "Seraphim" character your character could take the "Indomitable Will", "Dual Wielder", and "Jet-Jump Pack Certified" merits.
The Biggest "Elephant in the room" problem is the fact that unlike Warhammer Fantasy, in Warhammer 40k everyone is everyone elses enemy- but also will sometimes work together when the need is great. I suggest an "alliance of opportunity" system, wherein different factions can band together temporarily to wage war with certain other factions. Except to this rule would be "Polar Opposite" factions that would never ally, work alongside, or just agree not to shoot in the head the other under any circumstances: The Tau-Orks, Imperials-Chaos, Eldar-Dark Eldar. Each faction would thus have a defined enemy and also "allies", but Warhammer 40k being Warhammer 40k nothing would be certain.
