Space Marines in the Vineyard
I'm running this with the DitV system. The rules for gaining new traits will be a little more regulated to ensure our group can operate with them, and for purposes germane to the game's premise.
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Space Marines in the Vineyard
Marines work better for the DitV system than a lot of other options, I think; they have a command structure, and a nominal mission, so they generally have an incentive to get involved in a situation for better or worse.
Special rules would be as follows: a Space Marine automatically gets a 'super' trait, rated at d20 (oh so nerdy), called "Space Marine". If the player can make a good argument to fellow players and the GM that a Space Marine would be better in this given situation, he can roll it - it's just that when using it in raises, the player needs to have a suitably outsize description of what happens, like "I spit my Space Marine acid in his face, knee him in the groin, and pin him on the ground." You can't roll your Space Marine die unless it's a suitably dramatic action.
Dramatic Large Battle System
Since a fair amount of SMitV would revolve around leading troops into battle, I've innovated the Dynamic Large Battles in the Vineyard (DLBitV) system. Mechanically, it's similar to the standard conflict resolution in DitV.
Phases
Battle is broken up into phases: Parley, Long-range, and Close. The Stats rolled for the various stages of battle are different though - Heart + Acuity for Parley, Acuity + Will for Long-range, and Body + Will for close range.
Each is a specific conflict, and the winner of an early phase takes bonus dice to the next phase. Any unused dice from an early phase may also be carried over into the next.
Giving in a phase means termination of the entire conflict and that fallout up to that point is calculated. A Commander can't Give in the Parley phase and then initiate Long or Short range conflict - a phase must be played completely through, until one side has no dice left.
Commander
The Commander of a force will always be a PC Space Marine, or an Important NPC. They use their same Traits, whichever applicable for the current phase of combat. Note that two PC Space Marines cannot join into one force, and that a force composed only of a PC Space Marine or NPC is completely viable.
Soldiers and Forces
Solders are rated in dice, added as Traits to the Commander's Traits, and rolled at the time they're brought into play. Raises using soldier dice must account for the actions those soldiers take.
A Force is a composition of soldiers, basically just the list of extra Traits your commander can use in battle.
For instance, if your Force had "Veteran Scouts 2d8", and you committed them during the Parley phase, you'd roll the dice then, and probably do some raises against the information your scouts collected.
Miniatures
Ideally, the battle is played out with miniatures, on a tabletop space. Every raise involves moving some of these miniatures around; if the raise is the Commander's and a general tactical maneuver, the Commander can move any of his models; if it's only from Forces dice, then only the Forces whose dice are involved in the raise may move.
Fallout
Fallout isn't calculated until after the battle(?). Dice of Fallout cancel out dice of Forces or act normally on the Commander, at the Commander's discretion.