Hmm. That just gave me a cool idea (I have no idea how Sins works so this might be unfeasable) for different "paths" instead of standard upgrades. For example:
Knight Hammer track would decrease the upkeep cost and fleet supply each level, with the last level making it black and giving it extra fighter supply (as the Knight Hammer required fewer crew and actually carried closer to the number of fighters an Executor actually could carry if I recall)
Iron Fist track would increase hyperspace and sublight speed, with the last level giving it a one-time use "Save me" button activateable at low HP that would make it appear to be destroyed while actually jumping to the nearest capital shipyard (as the Iron Fist was used in hit-and-fades and that trick was used by Zsinj).
Reaper track would boost allegiance in your space and decrease enemy allegiance in theirs, with the last level also giving it an ability to generate a large amount of diplomatic points in other Imperial or Pentastar territory (as the Reaper was, in Imperial hands, used as a tool to attempt to reestablish faith in the Empire and bring wayward Imps "back into the fold.")
Lusankya track would provide a bonus against fighters and projectiles, with the last level giving it an ability to "activate sleeper agents" on a target ship, causing havoc in some way (as some of the heavy weaponry was replaced with more point defense systems and it was Isard's prison/reindoctrination center)
You can purchase any combination of these, but you could only get the highest tier if you invested all your points into that track.
I really love this idea.
For abilities, I think the SSDs should be offense-oriented, and the NR Star Dreadnaught defense-oriented with a defensive synergy with the rest of the NR fleet. Here are some ideas for the Executor:
Intensify Firepower: boosts firing rates but reduces engine speed and shield recharge rate/amount
Intimidate: lowers the stats of the enemy fleet in damage/chance to hit
Inspiring through Fear/Reckless Ambition: gives a sort of frantic feel to the Imperial fleet with greater engine speed and firing rates, but makes it take more damage/have less accuracy (this would be a refinement of the Iron Grip ability)
Point Defense: destroys fighters and bombers within a short range
The Numerical Superiority ability is very redundant, the Executor should already have a lot of fighter complement (upgraded as it levels up).
I like the Concussion Barrage ability as it is pretty much, though it could be more powerful to be better suited for anti-fleet action.
For the Sovereign:
All the abilities are very good, though the Mass Effect ability does nothing and should be redone. The Crack Mantle ability needs to be more damaging too.
For the Viscount:
Power to Shields: reduces speed and damage/firing rate but increases shield recharge rate/amount.
Sacrifice: forces enemies to target the Viscount in order to save your fleet from destruction.
Coordinate Efforts: the NR fleet tries to help and support each other, reducing offensive power but increasing the defense of the fleet (damage reduction, damage output reduction).