I spent unhealty amount of time in combat simulator and Detailed stats mod.
I change pilot skills by editing save game file, then let AI do the job.
I focus for shortest time to destroy all opponents, taking minimal dmg is bonus.
Result is :Energy mastery is weakest skill on the list. Any other skill has some measurable improvements (for certain ships), but this one not. If you have skill or not, deasnt matter.
For AI controlled ship, It only could help you in a way, that lost battles last longer.
For human controlled ship, It is theoretically possible get advantage in Phase Cloak ship, intentionally use this skill to uncloak on high flux and burst fire.
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A suggestion Energy mastery balance :
1. swap elite vs base effect
2. Change the range statement as fallows : Energy weapons deal up to +30% damage at close range, based on the firing ship's flux level. (remove the flux part).
If they apply both those changes, some of my pilots could use it.
Now, non of my pilots use this skill.