my sugestion for stealth:
instead of having stealth roles being a "you can hit" or "you can't hit" affair, why not make a failed stealth role result in a doge score for the stealthed ship (this dodge role ignores AF weapon's benefits and therefor is still usefull for fighters).
So every stealth score would have a target number that if defeated the stealthed ship can be fired on normally, amd a doge value that is applied if the stealth role is failed.
additionally stealth values should be generally increased, And possable values expanded to include numbers grater than 6 which would require stealth breaking technology (a scout, scanner to full, etc) to succeed at the stealth role.
Finally Stealth roles should be made before the player declairs his targets (after all you would know which ships you computer can and can't lock on to).
So for example a Minbari Sharlin might have tealth 8+/2+,
so if a Nova tries to broadside it the scenario may look like this;
first the nova captain tries to lock onto the Sharlin, but he doesn't have any stealth defeating technology so it is futile, however that isn't going to stop him from trying to shoot the darn thing out of the sky so he declairs all 12 AD will fire at the sharlin.
let's say he get's 8 hits
because the nova failed to break the Sharlin's stealth it hets a 2+ dodge, evaiding all but one of the 8 hits. The Sharlin takes signifigantly less damage than it would have had it not had stealth, but a determined capatain can still do damage to it without ever actually defeating it's stealth.
This way it can be made impossable/nearly imposable for some races to actually defeat the stealth of the more advanced races, while not totally disalowing them the ability to fight against stealthed enemies.