#1- I would like to be able to produce "Crews" to assign to starships. These Crews would come in five flavors.
"Research Staff"
"Medical Staff"
"Engineering Staff"
"Tactical Staff"
"Away Teams"
The size of the ship will determine how many crews you can assign to the ship. You drop them in at the time you launch the ship, much like you do when the colony ship or troop transport is launched, except any available crew on that planet are available to be dragged to the ships slots.
You can check a button to "Retain crew on every mission". If you check this button then the crew will stay on the ship even if they are orbiting a planet. If you do not then the crew is available for reasignment when you launch any ship from orbit. The crew stays on the world it landed on until it gets put on a ship.
These Crew provide benefits to ships. Tactical Staff add to the weapons, Engineering repair the ship. Medical not only protect crews from taking damage in battle but raise population on the new planet they land on. Research staff provide a bonus while in the ship of +5 RP and when they are on a world add +1% to the worlds research.
Here is where you can get tricky.
Give every race a "Racial Crew". This special crew can only be recruited by that Race. Star Rangers for the Humans, Star Knights for another race, Death Squads, Terminators for another, etc. I can flesh this out in more detail if there is interest. These unique crew are the ultra-elite of that race and reflect a special bonus. There may even be a limit of 3 per race no matter how big their fleets.
What would be awesome though, is if you capture the capital of the race that creates that world, then you can recruit their special unit. Sort of an assimiliation bonus. I always like to pretend I am a Zookeeper, collecting alien races.
Crews are randomly created based on the military budget being consistent and perhaps the make up of the planets structures. If you have a lot of factorys you'll get more engineering crews for instance.
Special Unique Structures like the Tir-Quan marine academy could also recruit unique units in the same vain except they belong to whoever controls that.
Lastly, Heroes;
Periodically have a Galactic Hero emerge. This takes up a single crew slot. "Zap Brannigan" types, who turn the ship into a super elite, or double its fire power or hp. They could even 'level up' and the player could pick which power they take.
You could also write a few events for each galactic hero (at least in the campaign) where for instance;
IF (Galactic Hero is on a world for 10+ turns)
"Doryx the Unquestionable has siezed control of the (world) and is claiming his authority comes from you, but he is the overlord of this world. Do you
A) Send your fleet immediately to demonstrate to this traitor what it means to invoke your name? (Planet Rebels)

Say "Yes...yes...he does" (Galactic Hero is removed, becomes a Governer, providing +14% planetary bonus)
C) Tell him to get back on his ship and stop playing (Galactic Hero gets the "whipped trait and loses 20XP")
something like this