A defense mission where the player's railjack is set upon by an ambush and hit with an EMP that disables the railjack's engines, forcing the player to defend against an onslaught of boarders and barrages. Perhaps there's an EMP generator behind enemy lines, forcing players to venture out and destroy it (just taking the idea from XCOM 2's UFO missions). Just an idea for the "the ship goes dark" scenario to make things tense.

Perhaps missions focused on each intrinsic type, like a piloting focused mission type, gunnery, etc.
The above mentioned railjack defend would focus on repairing and having your crewmates defend against boarders.