Currently, a player can make an excellent, small, fleet. Then win a single mission and unlock a vast plethora of upgrades with the huge honour reward.
Each mission has specific upgrades unlockable by completing it.
For example: Defending Sirius -> Cruiser Minimal Armour, ECM Shield, Frigate Armour 3
So the player completes the mission in normal and hard. He earns enough honour to buy two of the upgrades. Then, using upgrades from later missions, he returns and achieves more honour and buys the third upgrade.
This can be emphasized to the extreme. New players begin with only Frigates and Fighters and a minimal selection of modules. Oh no! Expert difficulty on mission 1 is too difficult. My Frigates and Fighters cannot succeed! So the player tries the next mission, progressively gaining upgrades until he feels he can return and conquer the expert difficulty. The player must carefully choose upgrades to assist his conquering of each mission.
This method will: Help to resolve players completing missions on all difficulties before moving on to the next. Thus all races are not unlocked at the same time.
Prevent players from unlocking most of the upgrades via a couple of small fleet, high honour victories.
Create a stronger feel of progression and reward, greatly needed given the lack of a story mode.
Prevent a ‘one strategy fits all’ fleet until many missions have been completed. The game designer knows what upgrades are likely to be
available to a player at each stage. Expert difficulty can be intentionally too difficult, if upgrades from later missions have not been obtained.
Allow for control over how difficult a particular upgrade is to obtain.
This method requires: Reworking the existing mission deployments to create suitable fleets for the player to face.
Assignment of honour to individual missions.
Assignment of upgrades to individual missions.
Deciding on an initial availability of ships and modules. Then locking the rest and assigning them to missions.
Cruisers need to become an unlockable. Indeed, why not have most specific hulls as unlockables?