You're missing the point. Yes, clearly skill B is better. However, if the player for some reason takes skill A instead, then the bonus to all ships component incentivizes using a larger fleet (and eventually the player will realize that they made a mistake and shouldn't have taken skill A.)
But Skill B is not clearly better. Skill A is superior for smaller fleets, skill B for larger fleets. Remember this is an "insulting oversimplification" and adding more ships to the fleet is not always better due to logistic costs and efficiency/player preference/fun (
going to back to what Alex is saying here).
Plus if I'm not mistaken, you're saying you want (for example) for skill A to be buffed from 100% to 200% for the player only. The result of this then would be:
Skill A is better for fleets with
less than 9 ships (200% vs 180%).
Skill B is better for fleets with
more than 11 ships (220% vs 200%).
... The end result is the same for which skill is better at which fleet sizes. The difference is my suggestion allows Skill A to scale, so in fleet sizes with less than 9 ships you're still encouraged to have a few wingmen rather than going solo. So what makes your idea The Solution
tm and mine Terrible
(c)?
Secondly, skill A is already different between the player and an officer, as the officer doesn't get the "all ships by 10%" part. If you're trying to avoid separating player and officer skills (and why would we be trying to do that, anyway?), then you've already failed. And besides, that wasn't the OP's suggestion; giving the player (and AI fleet admirals) access to stronger per-ship skills than a regular officer would get is completely different from removing per-ship skills and allowing the player (and AI fleet admirals) to assign an officer to their flagship.
Ah, but Skill A is different between players and officers in the same way it already is now! As it is certain combat skills unlock hullmods for the player to use for the entire fleet, whereas officers having the same combat skills don't. So there's precedence and cohesion is maintained!
With that in mind I think your idea of giving player version of piloted skills a stronger effect than officer versions is valid too, but I prefer mine for thematic reasons
: you're ultimately a fleet admiral, and you already have the option to be a stronger combatant than your officers by taking more combat skills than they can.
EDIT: also by separation of player and officer skills I mean having the two draw from entirely different pools with no overlap, essentially splitting one system into two systems... which is what OP suggested.