As I understand it, supply now takes the place of antimatter and is used mostly, or solely, for fighter construction (and is mostly regenerated by visiting something along the lines of a friendly resupply base/planet). If I'm misunderstanding things, some suggestions below may not quite make sense. Hopefully they do.
I'm also going to try to limit my number of suggestions to one per question-mark per ship, though a few will have extra suggestions.
Sovereign:
Passive: Terror -% enemy hull/shield restoration rate due to presence of such a terrifying enemy vessel demoralizing the enemy crews and reducing their efficiency
Active: Ram - Sovereign rams enemy vessel, dealing the enemy vessel's hp x 1.5ish in damage to both ships (allows it to kill smaller ships without much risk, but pretty much guarantees both die if it rams another titan-class)
Executor:
Passive: Terror - same as Sov. above, maybe smaller bonuses per level since the Sov's superlaser makes it extra scary
Passive: Fleet command - % bonuses to damage dealt plus sharing damage from nearby friendlies, as the Executor's command staff manages the fleet and rotates ships off the very front lines for R&R
Passive: Massive hangars - allows it to replace destroyed squadrons more quickly as well as adding to its normal fighter count
Active: Intensify fire - Focuses all fire on one target, granting 200% damage against that one target but cuts all other weapon banks to 50%
World Devastator:
Active: Construction - requires an unused asteroid (such as one in a gas cloud that lacks a colonizable planet), allows the ship to act as a frigate shipyard at 75% construction speed due to limited materials. I'm guessing this would need to work mostly like the capture ability does for them, while adding a faction-wide modifier - probably a pain in the ass to code, but it just seems right for them so I have to suggest it
Active: Tractor beams - enemy ships (up to, say, 4?) cannot move or hyperspace
Active: Absorb - consumes enemy frigate, regenerating hull damage equal to target hull x 1.25 (provides an incentive to micromanage and target enemy ships with the most hp without punishing those who choose not to)
Praetor:
Passive: Fleet command - similar to Executor, maybe regenerative rather than damage based to differentiate (and work better with bulwark)?
Active: Covering fire - the Praetor uses it's long-range batteries to distract enemy targeting, providing nearby ships with an evade/damage reduction bonus
Active: Barrage - temporarily grants the ship 150% weapon range (maybe 200%?) but with a 25% drop in damage dealt
ISD2:
Passive: Fleet command - again, similar to Praetor and Executor, but perhaps again with different bonuses, maybe this time supply regen
Altor:
Active: Refurbish - Uses ALL Altor's current supply, friendly vessel gains % damage dealt/reduction relative to Altor's supply for some amount of time (maybe only works on cap ships, NOT titans, so that the bonuses can be scaled appropriately - it seems fitting that if an Altor spends all of its materials upgrading an ISD2 or even a Praetor for combat, they'd be fantastic until munitions and spare parts began to run low for the extra systems, but an SSD shouldn't receive anywhere close to the same percentage bonuses that they would considering its incredible size)
VSD1:
Active: Salvo - VSD fires its entire complement of concussion missiles at one target, dealing massive damage (not sure how Sins works by any means, but ideally I view this as essentially granting the VSD a full missile volley at around 150% normal damage, while resetting the reload period for its missile weaponry and adding a couple seconds on top of it)
Passive: Bombard - given the atmospheric capabilities of its design, the VSD is able to get closer to the surface and deliver superior precision fire to ground targets
VSD2:
Passive: Bombard - same as VSD1, maybe a higher modifier due to ship upgrades
Active: Microjump - the VSD2s enhanced engines and navigation systems allow it to make micro-hyperspace jumps within systems, allowing them to suddenly appear at their enemy's flanks (essentially the Vasari loyalist's Titan ability)
Dreadnaught:
Active: Ram - Ship deals 2 x own hull value to itself and target (in memory of the ISD Peremptory)
Strike Cruiser:
Passive: Extra hangars - researchable passive, post-construction modules add additional hangars to the cruiser, granting it extra squadrons
Carrack cruiser:
Active: Power to engines - ship's speed is increased for a short time, NO negative modifiers to other systems but can only be used once between resupply visits
Passive: Mosquito's bite - ship has damage dealt/damage received bonus against enemy titans (small enough to not attract much attention from the enemy ship's weapon banks, yet able to cause an itch)
Acclamator:
Passive: Bombard - similar to VSD1
Passive: Extra hangars - researchable, self-explanatory
Active: Deploy stormtroopers - applies boarding effect to enemy frigate (nothing else seems to have it)
Lancer:
Active: Fighter tractors - researched ability, Lancer frigates are equipped with small-ship tractor beams that, while unable to fully capture enemy fighters, limit their maneuverability and grant the Lancer a 50% damage bonus against them until the generators need to initiate a cool-down cycle
Active: Screening fire - The Lancer focuses all guns on protecting nearby friendly capital ships, giving it a 50% damage bonus against enemy bombers, though reducing damage against enemy fighters by 75% due to the firing delay involved in synchronizing fire from multiple batteries
Passive: Superior ion drives - Later model Lancer frigates were able to keep pace with an X-wing squadron; this researchable upgrade allows yours to as well (I can't recall the source for that claim though it was most likely an X-Wing book, and it may be that it was Y-wings instead of X-wings, but I'm certain I recall a book describing Lancers as equal in speed to one of them)
Vindicator:
Passive: Patrol - The Vindicator's speed and size make it an excellent system patrol vessel, and the presence of one consoles the public, granting an allegiance bonus of, say, .2% per ship (allows you to really buff allegiance in a place or two with a couple dozen frigates, but requires significant investment to do so)
Active: Intercept - the Vindicator makes a microjump toward an enemy ship (if possible, placing it directly in the line of travel of target), attempting to prevent its escape
Viscount:
Active: Power to shields - shield regen gets % buff, weapons and/or engines get lesser % debuff, would need testing to work out a fair compromise given the scale of Titan/Super-class ships
Passive: Fleet command - Again, fleet buff
Active: Fleet navigation - allows FLEET microjump, having every friendly combat ship within X radius of Viscount instantly jump to relative point from target location (I have no idea if Sins would even allow this to be possible, but it'd be sweet)
Active: Deploy rescue shuttles - instantly collects all escape pods in current gravity well, gaining all their bonuses until a reasonable limit is reached
Nebula:
Active: Power to weapons - I liked it in ICW, I see no reason I wouldn't like it here; % damage bonus, lesser reduction to shield/hull regen and speed
Active: Deploy troops - massive damage to planets, but requires resupply to reset cooldown
Active: Duel - focuses all systems on one enemy target, granting 200% damage against that target as well as 50% damage reduction from that target, while reducing damage to all others by 50% and increasing damage taken from all others by 25% (numbers to be modified as needed, the goal being to make it an ideal one-on-one fighter against enemy capital ships in the early game while being an ability that actually seriously weakens it if used in large-scale engagements)
Active: Deploy K-Wing squadron (deploys a friendly K-wing squad to the local gravity well independent of the Nebula's resupply, and it would decay over time like any fighter squad lacking resupply - ability upgrades could be either extra squadrons or longevity upgrades)
Endurance:
Active: Scramble - launches at once every fighter and bomber the Endurance has, totally draining its supply (upgrades would give the fighters and bombers damage given/taken bonuses for increasing time periods, or perhaps extra ships per squadron)
Active: Deploy rescue shuttles - rescues all escape pods in the area, receives significantly enhanced supply regen (allowing more fighter launches) per pod but gains NO other bonuses from them (idea being that it is rescuing friendly ejected pilots rather than capital ship crews)
Passive: Expanded hangars - extra squadrons, similar to the base Sins ability
Passive: Starfighter command - damage taken/dealt bonuses for friendly fighters within radius, both increasing with upgrades
MC90:
Passive: Fleet command - you've seen it before
Active: Torpedo barrage - A torpedo volley is perfectly timed while the enemy's defensive systems are distracted, and a brace of torpedoes manages to bypass the shields and directly damage the hull, doing X damage
MC80:
Active: Fleet defense - Accustomed to shielding friendly vessels from enemy fire, the MC80 absorbs 50% of damage directed towards nearby ships, while only actually suffering 50% of that damage itself (numbers open to balancing, as always)
Assault Frigate:
Active: Fleet screening - Pretty much the same as the MC80's fleet defense stat-wise, the idea being that the MC80 is simply getting in the way, while the Assault Frigate is maneuvering both boldly enough to gain attention yet erratically enough that it's avoiding much of the fire
Active: Boarding party - shuttles of New Republic marines launch for enemy ships, attempting to gain control of vital areas
Bothan Assault Cruiser:
Active: Torpedo barrage - similar to MC90, though since I assume the BAC is a frigate and the MC90 a cap ship, I'd place the BAC's torp barrage damage above the MC90's base ability damage, but around or just under the MC90 level 2 torp barrage damage
Passive: Bothan spies - 1% chance (maybe, probably less) that any enemy frigate coming within range will self-destruct, any enemy cap ship take 750 hull damage. Only applies once to any enemy ship per encounter (meaning encounter within gravity well: if ISD Avenger pops into my system far from my BACs, nothing happens; if Avenger closes with the BACs, per ship it runs the RNG, and passes, so no extra damage is taken; Avenger withdraws anyways, BACs don't pursue, and if Avenger now turned to fight again it wouldn't risk another run at the RNG; but if Avenger jumps out then comes back, it DOES risk another run at the RNG per BAC)
Proficient: (I may be underestimating how strong you've made this ship, since according to Wookiepedia it seems to suck without special modular systems, so my upgrades are meant to make it potentially strong in various ways)
Each ship of the class gets ONE upgrade from the following, selected after construction
Extra hangars - gains two fighter, one bomber squadrons
Extra guns - another 20ish heavy turbolasers are added to the ship, making it an equal match for most ships its size (or however many would be needed)
Buzzdroids- Allows the ship to instantly deploy a field (5-15 depending on strength feels right to me) of droid-mines able to home in on enemy ships
Gravity well generator - self-explanatory
The idea really isn't to make it more powerful than it should be lore-wise (since I don't recall it from anything and thus have no idea beyond the Wookiepedia entry on how strong it should be), but to make it hard to predict - a fleet made entirely of Proficients could with the above be anything from fighter heavy to mine layers to a heavy frigate line to an insane mix, and until actually engaged it'd be hard to tell what you're up against. Ideally, against that pure Proficient fleet if you've prepped even decently for it, you should tear through without trouble, but if you load too many Lancers and they've got only a handful if any ships set up as carriers, much of your fleet is suddenly of little worth. The NR fleet's strength was versatility, and I think it'd be fun for this somewhat lesser-known ship to help exemplify that.
MC40:
Passive: Superior engines - Is faster than expected for a ship of its size, able to catch most frigates in a chase and easily run away from larger enemy ships
MC30:
Active: Cluster bombs - rather than a torpedo volley at ships in range, does massive damage to enemy fighters in range
CR90:
Active: Power to engines - grants the ship incredible speed, showing why it is known as the blockade runner - nothing can catch it during this heavy burn, not even fighters or missiles
Passive: Corellian design - grants the ship one of a selection of passive upgrades, either increased normal speed (does not apply to PTE), superior evasion (-% damage taken), or mid-ship lasers (if its base armament is mostly turbos, it gets some quads, and vice versa - don't know exactly how you're doing it, but the idea is take what's missing and add a little of it)
Nebulon-B:
Active: Engineering crews - repairs hp/shields/both of nearby friendly ships
Active: Graduating class - gives friendly ship a supply bonus, allowing it to launch more fighters before returning to base
Passive: Medical frigate - adds to base regen rates of nearby ships as injured crewmembers are gotten back on their feet faster
Quasar:
Active: Scramble - drains supply entirely, launches all possible fighters/bombers at once - similar to Endurance ability, but not as good since it lacks the damage dealt upgrades
Passive: Covering fire - quad laser batteries provide cover for the launch vectors of its fighter and bomber squads, granting them a 30 second window of invulnerability after they launch (useless in most situations, since the fighters will launch and lose the bonuses well before contact, but if you happen to end up dropping a couple quasars right in the middle of an enemy fleet the abilities form a nice combo)