Put simply, Faction Modules should apply to ALL ships, not just Secret Projects.
This could be done in one of two ways; either the Faction Modules apply only to primary roles (ie: Empire Recons, Gunships and Long Range Frigates get Faction Modules; Empire ECM, Command and Engineer do not) or all roles within the faction.
Each Faction should have a clear and distinct theme in how they go about things; suggested themes are given, along with suggested modules.
The factions should be split into two groups - one that focuses on direct power and damage, the other that focuses on indirect utility. This is not a set-in-stone rule, however.
Legion, Vanguard and Raid should be primarily about direct bonuses - more damage, more resistance, etc.
Wardens, Armada and Techs should be about indirect bonuses - reduced cooldown, better debuffs, etc.
The following is not an exhaustive list, but just some ideas that are based, in part, from what I remember about the original Faction Modules. I’ve also taken a page out of the Secret Project ships where I can.
Microwarp spool up time reduced to 0.5 seconds.
Microwarp spool up time increased to 2 seconds. Stuns all enemies within 300m for 2 seconds upon activation.
Breaks all active locks on ship when Microwarp is activated.
Jump time extended to 2.4 seconds.
As normal Overdrive. In addition, increases all Hull Resistances by 30pts for the duration.
As normal Overdrive. In addition, cancels all negative effects upon activation.
Speed, Acceleration, Turning, etc. increased by 75%
As normal Overdrive. In addition, increases all Shield Resistances by 30pts for the duration.
LONG RANGE FRIGATE MODULES:
Damage increased by 10%.
Deals 80% of damage on impact, and an additional 5% damage per second for 4 seconds (total damage inflicted is identical to normal Disintegrator).
Raid Guided Torpedo:
Explosion radius increased by 30%.
Techs Guided Torpedo:
Torpedo fuel increased by 10%. Torpedo speed and rotation speed increased by 30%.
Drone damage reduced by 20%. Ship controls up to three Drones at once.
Drone durability increased to 3,500pts.
Drone damage increased by 10%.
Drones destroy incoming missiles. Drones are destroyed in the process.
Addendum: Reorganisation of Ship Tree to make best use of above changes:
Ship tree adopts the T5 model of “Primary-Secondary-Primary” for ALL tiers.
However, faction positions swap in various tiers. For example: here is a sample Empire Fighter progression.
Rank 1 - Empire Gunship.
Rank 2 - Legion Command.
Rank 3 - Wardens Gunship.
Rank 4 - Empire Gunship.
Rank 5 - Wardens Command.
Rank 6 - Legion Gunship.
Rank 7 - Empire Gunship.
Rank 8 - Legion Command.
Rank 9 - Wardens Gunship.
Rank 10 - Empire Gunship.
Rank 11 - Wardens Command.
Rank 12 - Legion Gunship.
Rank 13 - Empire Gunship.
Rank 14 - Legion Command.
Rank 15 - Wardens Gunship.
By reversing roles in each tier, the game’s meta changes from tier to tier as the ‘top’ ships have differing Special Modules.
This pattern can be varied between races. For example:
S - Standard.
F1 - Faction 1.
F2 - Faction 2.
EMPIRE: S-F1-F2 S-F2-F1 S-F1-F2 S-F2-F1 S-F1-F2
FEDERATION: S-F1-F2 S-F2-F1 S-F2-F1 S-F2-F1 S-F1-F2
JERICHO: S-F1-F2 S-F1-F2 S-F1-F2 S-F2-F1 S-F2-F1