A simple storyline tweak would fix this as well. Something along the lines of "As the conflict with the Drengin Empire was warming up, humanity found themselves sending out colony ships to remote sectors. Different leaders will find themselves in different circumstances, facing different challenges, as they move through the unfolding campaign against the Drengin--and worse."
You could integrate this into more of a persisting thread throughout the campaign:
* Specific leaders for the campaign would be customized (meaning the leader abilities are hardwired, perhaps, rather than player designed).
* The same leader wouldn't play every campaign, but some leaders would make more than one appearance in a campaign.
* Leaders could bring their technologies forward with them? (bringing units forward would see silly)
This would obviously mean the need to redesign the scenarios, but it'd be mroe fun that a number of stand-alone scenarios linked by an interesting but--for that part of the campaign that I played--fairly predictable and formulaic storyline.
The scenarios themselves seemed reasonably well-designed, but the backstory felt more like an excuse to jump through the hoops outlined in the victory conditions for each scenario than an epic saga in and of its own right.