One of the options I am currently investigating is to use player loadout to shape the missions. If my PC hadn't gone down you would have seen the first iteration in The Lost Generation, spoilers below:
TLG Mission 10, WIP name "Dark Amaltheia"
The mission revolves around the NTF attacking the Epsilon Pegasi-Capella Blockade. However the sorry state of NTF Command throws a wrench into the planned operation and the attack force lead by the NTD Vasa has to make due.
During the loadout you have the option to pick either a Zeus or a Medusa as your bomber. The mission checks that choice in the beginning, and then has two tracks for the mission to progress.
If you picked the Zeus, your objectives will be taking out subsystems on enemy capital ships (disableing the Mjorlnirs) as well as turrets (allowing ship to ship combat). Additionally you will be tasked with helping against the bombers launched from the Messana.
If you picked the Medua, your objetives will be more focussed on taking out Cruisers/Corvettes and the Mjolnirs at the node.
The whole thing is still unbalanced (the Medusa path is easier despite the Medusa) and needs a little work.
Of course, these things can be adapted with the proper introduction in the briefing, as well as more meaningful shaping of the mission...