Thanks for that answer Majestic7. That helps a lot.
So, here's the plan so far (though I'm not very far in). Consider this the "what I hope to achieve" roadmap. I'm going to be developing a very generic "space army simulation game" in unity (as if I were to make a WH40k game I'd probably be shut down by GW's trigger happy lawyers). However I'm building it to be highly moddable from the start (even my primary content which I intentionally don't care about is going to be a mod). It will let you pick which mod you wish to play when you start up the game (much like Mount & Blade Warband's launcher).
Each Mod will contain:
-a splashscreen image.
-a map generation file where you get to define system types, planet types, (and frequency) and map size.
-a factions folder where you create all playable and non-playable factions for the game
-a faction will declare its army structure, its units, its equipment, and either pick an existing ai type or have the ability to create your own ai.
-factions will also have an "affinity" group and value(so most human/LSM factions could have an affinity to the imperium group, CSM and deamons can have an affinity to chaos, etc.). This really just affects starting diplomacy, though in the future we may have a "loyalty" value based somewhat on this.
-and factions will contain events that can happen to them (I will have to make this related to a faction in order to let the wh40k mods get lore right).
When you play the game, just by this engine's nature, you will be picking which factions are present in your game. While some people may really like this feature ("yay, no [insert faction you hate here]"), I feel that it would be beneficial to have a "standard game" (how the mod was meant to be played) as well. So I'll try to implement that into the mod system later.
After I get the base game working (it takes a bit longer to build modularly like this, but I have hope) I plan on releasing it to the community so that people with unity experience (and hopefully those without) can begin working on mods. I then hope to make a tool so that you don't need programming experience to make a mod.
Lastly I hope to create a way for mods to have "dedicated factions" (such as existing chapters) and "alterable factions," this way there can be features such as creating your own chapter in the game (instead of via modding tools).
That's the roadmap I hope to manage. I'll keep you guys informed of progress. Wish me luck!