To me, the back story and lore would be more important than having a fun and challenging campaign (simply because there are already so many fun Sins maps, but no back story except for the little description of the map, the description of the sub faction and what is found in the intro video and manual). But if it was possible to have both, by all means, both is better.
I would actually prefer if the campaign forced me to play one faction. I think that without this it wouldn't be much of a campaign, more of a scenario.
Concerning the having to play a modded version of Sins, I would prefer it if it was straight vanilla Sins Rebellion, but if you added something like a fortress world for, say, the Vasari's nemesis, and made it look lore-friendly, I would not object. But to add a faction out of the Sins universe, or to add more ships to the existing factions, well, I would rather not. But to add a unique ship that you have to escort, and made it faction-fitting, I think that would actually enhance the appeal of the campaign.
I think that a linear campaign would allow for a higher degree of quality, so I would shoot for that.
If you are actually volunteering to do this, Seleuceia, you are awesome. If you actually finish it, and it is amazing, as Sins deserves, then you are triple awesome. If you are trolling, well, suffice to say you are very far from awesome.