Possible idea: make so that most skills (especially those related to single-ship buffs) have mutually exclusive "personal" and "fleet" versions.
Ie: the "tree" for a single skill could be, as a simple example
Lv1
/ \
Lv2 Lv2
(personal) (fleetwide)
\ /
Lv3
The "personal" skill is of course, much more powerful than the fleetwide one, but is only applied to the ship you're piloting.
Officers can, of course, only get personal skills.
Here's the kicker, only the bigger bonus applies meaning that the fleetwide stuff is great if you want to command a big horde of scrap and run somewhat lean since you don't have to deal with officer salaries (quantity over quality approach) while it becomes nearly useless if most of your fleet has officers (since only the bigger bonus applies).
Or you could pick more personal skills and get your other ships officers (quality over quantity approach).
This is to be combined with a removal of the fleet cap and likely with an increase in officer costs, you can have a whole lot of slightly buffed ships or be a small-ish elite team where every ship (including yours) is as buffed as it can be without forcing the player to be just a buff machine while the officers get all the fun because otherwise your fleet can't survive the triple stacked deathball the AI is allowed to run at zero cost
As for the trees:
Combat: kill stuff better and be more resistant to being killed, magazines, armor, shields, missiles, you name it, we got it (offensive and defensive buffs)
Leadership: get stuff where it needs to go fast, whether that be ships, fighters or ammunition, also command points for days (the "speed" tree)
Science: nasty ewar stuff and toys to troll your enemies with, debuffs go here but there's also other stuff (battlefield control & co.)
Industry: the ability of having stuff working smoother than before, what are these "critical malfunctions" you speak of? (endurance tree)