It's an interesting concept, maybe not complete invisibility, but something more along the lines of adaptive camouflage.
http://www.popsci.com/scitech/article/2006-09/first-invisibility-shield for example.
I am not a modder, but I've been a muse of sorts to modders with other games. So forgive my ignorance.
Is it possible to set the color of a ship to be that of whatever space it's in? So it mirrors what the environment is beyond it? I guess so, if you look at stealth or invisibility in games such as City of Heroes/Villains. But is it applicable to non-developers?
The texture of the ship model is still there, so it can be vaguely made out if you're visually scanning for it. If you know one is out there, one can find it, but intially, a great first strike means.
An easy balance to this feature would be an implemantation that could be sold (realistically) via sonar. This would be an excellent tactic for non-colonizable planets and otherwise "empty" space, but for the cliche planet capture battles, near useless (a sonar tech of some sort, attached to the inhibitors (much like the tachyon). Another built in preventative to making this ship too powerful would be to apply Star Trek canon...
Plasma Storms for example, can pull the ship out of cloaking.
Sorry, just brainstorming.
Edit: it's canon, not cannon. Sorry if you caught that. 