Hmm, well I haven't been able to try it out yet, as I want to finish my current run first, but I have an idea as to what determines which spell to use. Does it have to do with officer disposition perhaps? AKA, steady officers (and the player) get Zephyr Ray, reckless officers get White Destruction Field, timid officers get Balanced Scales? That would explain why most ships get Zephyr Ray - ships without officers default to it, and you usually don't have an officer in the simulation.
Hoho! It seems we have a winner!
Indeed! For your officers, the spells which they use are determined by their personality!
Reckless officers use
White Destruction Field, since they get up-close into the enemy blob
Aggressive officers use
Aether Rain to pick off one ship at a time
Steady officers use
Zephyr Ray to force enemy ships to overload
Cautious officers use
Seeker Orb for long-range fire support
And
Timid officers stay safe in the back, using
Balanced Scales to equalize your entire fleet's Flux gauges every 40 seconds!
Congratulations! May I use your username as the discoverer of this secret?
And you are quite right that it does not explain how the player decides which spells to cast! Well, in campaign at least - since in missions, it is possible to set special officers with personalities, and if you use that ship there, you can, as the player, "have" that personality.
So, with that, here is a follow-up secret:
Since the player does not have "personality" (in the campaign), how do you determine which spell you use?
Finder: None yet!
Clue: It's a different system which determines a 'personality' for the player. Easymode: Yes, your 'personality' can change.
Secret: ??
And lastly, I haven't tried this system with the mod that changes your officer personality! Maybe it'll work?
Edit: No, it's not factionwide aggressiveness, since it can be possible for a player not to join a faction.