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In this question about manned spaceships versus drones, a user (perhaps jokingly) pointed out that "manned" wouldn't technically be correct when talking about an extraterrestrial spacecraft:
By definition, they wouldn't be 'manned', but they might be 'aliened'.
Potential jokes aside, is there a more species-neutral adjective we can use here?
Consider crewed, which means:
Provide (a craft or vehicle) with a group of people to operate it:
'normally the boat is crewed by 5 people'.
It works perfectly in a sci-fi context. For example,
The ship was crewed primarily by Vulcans and cyborgs.
Piloted would seem to fit nicely, although it does have to connotation of having a pilot rather than just a passenger.
Staffed could also work if you didn't want to talk about a specific pilot rôle.
Operated would also take out the species element of the word, focusing on the job.
Occupied would do the job:
One of the meanings of occupied is:
Being used by someone; with someone in it.
The craft was occupied.
Inhabited
What are commonly called 'drones' are sometimes called 'uninhabited air vehicles' as unmanned also means 'cowardly' so is not a selling point for combat aircraft; the inverse of this would be inhabited.
Most UAVs are piloted remotely or autonomously, so 'piloted' does not imply inhabited - the Reaper is piloted, the V1 was not, neither was inhabited. Similarly, in military speech, UAVs also have a crew - if you are the remote pilot or weapons control for a UAV you are still considered its air crew, and every UAV also has a ground crew:
The primary concept of operations, remote split operations, employs a launch-and-recovery ground control station for take-off and landing operations at the forward operating location, while the crew based in continental United States executes command and control of the remainder of the mission via beyond-line-of-sight links. USAF MQ-9 Reaper fact sheet
In order to properly leave anthropocentrism behind, you have to think outside of the...ugly bags of mostly water. Otherwise you are making assumptions that are echoes of that anthropocentrism.
The Greebbllaapp vessel originally consisted of several semi-sentient modules that wandered desultorily around the galaxy extracting iridium, but its frighteningly malign intelligence did not fully emerge until the assembly became infested with quintillions of mutated nanomachines.
Whether or not the greebllaapp can be considered 'living species' or not is debatable...But if you must talk about a 'major interstellar war' going on between biologicals, then one of the combatants might well say their enemy's ships are 'infested'.
