In all my battles invisibility was heavily broken, every single time.
1. I can see any supposedly "invisible" enemy ship. They are translucent, but quite clear target. And while they can be hard to hit initially, first hit removes invisibility altogether. Too bad for such expensive technology. Consideration: maybe it's wrong to remove invisibility altogether, if only invisible ship is not attacking itself?
2. Well, I know that it could be my too-advanced technology, and in _other_ battles it's all different... but if it is not, how about forbid to target invisible ship at all - until it will be detected with scanner advanced enough, after that it became targetable... but still a hard target?
3. Every shielded ship have it's shield up right from the start, and any invisible ship haven't shield at all until next turn, even if it possess it. That makes invisible ships much easer targets than shielded ones. Consideration: rise up shields instead (non-working anyway!) invisibility generator after disrupting. (Of course, if you'll take approach in p.1, when there is no disrupting on hit, you doesn't need this).