With the understanding that the odds of me being able to sneak a skill revamp into 0.9 are right around zero, I like how this sounds! The in-fiction justification is very much my kind of hand-waving, too
Hmm. I think it might work more cleanly if it was, say, +1/2/3/4% for destroying a ship of a specific size, up to a total % limit. Calculating/conveying hull damage percentages seems like it'd be messy.
So, let's see. Good things: scales up combat power based on flagship actions, gets stronger in larger battles. Bad things:
Nothing comes to mind right off, but still, would have to think it through more. Not entirely sure a damage bonus (that's got a reasonable cap, anyway) is major enough.
Stepping back for a moment, I think there's a psychological component here as far as combat vs other stuff. That is, it feels bad to have officers be better than you skills-wise, and the flipside of that, not being able to get significantly/at all better than a maxed-out officer.
I think if combat gave some bonuses that only the player got (i.e., say an extra bonus at tier 3 that's player - or fleet commander - only), then it'd
feel a lot better, even if the actual overall power balance remained about the same. That might also lead players to give combat more of a fair shake; while I do think it's a bit weaker, I think it also gets dismissed much more than it should be.
"Deconstructive Analysis" fits right in with this, too, so that's very nice. Ah, hmm - you know, this might actually work better as a 3rd/player-only tier of a skill rather than a standalone skill.