As the commander of the U.S.S. Enterprise here are my thoughts on the harbinger update and future updates.
Drones:
In the game drones are a major part of the game and thus we should add a few things to make them interesting
New interface
In the first game we had the opition to modify the weapons of drones without replacing them all together and they were capable of using shields. So a new GUI system could be added for the drones to give the commander opitions on the kind of weapons and defences they have. Regarding the upgrade section they could have things like armor and number of drones you could have. Although this kind of thing can be difficult to make so we will go on to the kinds of weapons a drone can have.
Missles: this seem sound and logical since in the last game drones had this as well, however they will interact with shields and should do little damage to the shields but heavy damage to the hull to make it fair.
Gattling gun: Although was not used in the first one a gattling gun is still used on large ships and are capable of mounting one or two on a drone to focus down enemy drones.
Orb: In the last game the orb was similiar to what an energy cannon could do but it had a very nasty punch but a slow recharge time.
Suicide: These drones were filled with bombs that would make the drones ram into enemy ships and explode doing heavy damage but sacrificing the drone in the process.
Electrical magnetic pulse (EMP): Its a device that could be used to completely disable enemy ships basically stunning while your ships main cannons pounded on the enemy fleet.
Nova: an energy based weapon that release an energy blast that can do area of effect damage to groups of enemy ships.
Boarding party: Drones could have marines on them that ram into enemy ships to attempt to hijack enemy ships and take control of them.
These are the ideas for weapons but we should also look at defences.
Shields: this was an opition in the previous one for drones to have equiped and this made it possible for drones to survive longer in combat.
Cloak: This allows a drone to disappear making it almost impossible to detect until they start firing.
Micro repair bots: microscopic robots that help repair the drone very slighty to help it survive better in combat.
Drone commands
In the 1st game drones had many opitions regarding what to target or whether to fight or evade and whether to focus fire on something however there should be a few more to look at.
Defence line: Drones use their current weapons to intercept enemies and stay at certain points to shoot down energy projectiles, missles, or even the dreaded nuclear weapons, etc.
Aggresive: Drone charge ahead ignoring everything around them to destroy one target.
Evasive: will attempt to distract enemy fire and out menuver them is possible.
Disable: drones will disable enemy ships by destroying turrets, shield generators if any, and hangers.
And to top it off what about using alien drones to make yourself more unique with unique disadvantages and advantages
Turrets
Although there are alot of interesting ideas on weapons more could be added for ships.
Tesla coil: Mainly used as an anti projectile based weapon system and if close enough can be used as an energy based weapon.
Mine layer: leaves behind mines in space that can be used like a trap
Anti-drone field: Weapon system that hacks into enemy drones and use them against large ships or make them attack each others. (Also potential to hijack them and use them as your own).
Factions:
Another idea is to add in different factions of aliens that fight each other.
Mercenaries: this idea might of been mentioned but, being able to hire mercenaries for x number of days makes combat interesting
Clans: Groups of aliens that are unique and are capable of being flat out enemies with humans or potentially allying with huamsn and trading their merchandise with them, or even ships.
Reinforcements: this idea might of been mentioned, but being able to call human and/or allied alien ships to help you fight would be interesting to see.
Base creation: It would be very neat to help build stations of your own to lay claim to a part of space (and having the enemy do the same as well).
Black market: ports where you can buy items normally not available to you or allies.
Bounties: While doing your tasks you might get a secret messege from an alien to do assignments for them like capture an alien commander or killing someone off in return for resources.
There are more things to say but at another time