I was just about to post my own special houserules, when I stumbled upon this topic and realised that Moribund had come up with quite similiar ideas.
Allthough we both reduced armor by 12 and tread each Makro hit seperatly vs. armour, I did some further changes to fighters and the lot.
I'd like to present my rules and discuss them :-)
Void shields: Shield ratings counts like toughness bonus in groundfights. I.e. shield rating of 1 will substract 1 point of damage from each and every hit with a macro and lance.
Torpedos: Substract 12 damage, vortex stay the same. Torps ignore shields, which makes them even better vs. capital ships.
Lances: Get armour penetration of 8. They would be designed to ignore armour up to the level where normal warships wont get further layers of adamantium.
Broadsides: Receive a +10 to hit Bonus and follow the Rules for full-auto-fire. I like the storm-rule of Maribund, too, but saturating fire should have a higher chance of hitting eldar.
Fighters/Fighter-Bombers/Bombers: Speed 10/9/8, bonus/malus of +10/0/-10 to hit and evade, damage vs. ships is 0 / 1d10 / 1d10+2. They generally ignore void shields once they are close enough to a ship. They can stay in combat for hours without need to resupply.
Shooting at small craft / torpedos with macros or turrets: Shooting with makros has a malus of -20 to hit. Shooting with turrets (i.e. crew value +10 for each point of turret rating) only possible at 1 VU. Shooting at small craft suffers a further -x to hit, while x is the netto-piloting value of the small craft pilots. Each succes scored to hit removes 1 torpedo or 1 wing of attack craft.
Dogfighting: Compared Piloting test by both sides. Winner destroys 1 wing of fighters for each succes. Same goes for torpedos, estimating their piloting value to 0.
-> so small craft lack in fire power vs. medium or heavy armored ships, but make up in mobility, evading hits while drawing fire plus are a quite formidable defence vs. other small craft and torpedos.
Evading hits: Just like groundcombat evasion, you roll piloting + manouvre and each succes evades 1 hit of makros or lances.
Rak'Gol: each natural 10 on the 1d5 (aka 1d10/2) damage dice will reduce their targets armor value by 1, due to grinding off the armour.