I hope the bonuses are small enough to not be game breaking, sort of like how the 'Reward Perks' in new vegas worked. Killing 200 enemies increased damage by 1%, killing 500 gave +2%, killing 1000 gave you +4%. I believe the bonuses shoudl be small and not absurd enough to break the game, only really slightly tilting the favor.
Also sinc ethere are admiral upgrades, will there be ship upgrades? Things that you can buy tha greatly increase the performance but only on a single ship and if that ship is lost then you lose the upgrade on it along with the ship itself. It could be something like 2500 credits gets you a MK2 Lasher Engine that boosts speed by ten units with no drawback or cost other than credits. Small, and you can't buy 5 of them to get 50 speed, but it's a small bonus to make things more interseting. This also can allow you to compensate for lacking technology and combat trees, you can compensate with your industrial ability to create credits to make up for the lack of technology in that area.
Also you said there are ten skills, are they applied to all ships in the fleet, only yours, or do you have to pay to apply them to a ship? Part of me wants the flagship to always get all the bonuses but for other ships in the fleet you have to upgrade them at cost, but much MUCH lower and conveniant than going out for a ship modder factory that overcharges you for meager upgrades to system performance. Some should also simply not be available or possibly free to those who heavily invest in such an area.
Also can we get a summary of what each tree involves in terms of it's bonuses so we can have some sort of idea what we're getting ourselves into?