How about reworking the Chameleon module(s) altogether? If we consider how it would work IRL, we could use some of that to both improve it and make it less effective for certain situations. Here are a few things I think could be done:
First, active stealth only renders you invisible within the spectrum of visible light. However, weapons targeting systems often operate within the infrared range, so active stealth wouldn’t really do anything to block targeting. Therefore, missiles & AI weapons would remain locked onto a target even if it went invisible. However, for the sake of some additional benefit, AI weapons could take, say, twice as long to lock onto an invisible target, and perhaps missiles may need a few sec to lock-on, so ppl can’t simply scan the entire battlefield and instantly expose stealth targets.
Also, if a craft has a large physical presence, then a radar would still detect it, regardless if it’s even visible to the human eye. Therefore, active stealth does nothing to help you escape detection from radar.
Now that the Chameleon is pretty much useless by this point, we can finally get to making some improvements. First, we can increase the duration of active stealth by a significant amount, maybe 10 sec for Mk1 & 15 sec for Mk2. Next, its deactivation when firing or taking fire could simply be disabled, as it’s not really hiding them from radar or AI/missile weapons anymore.
Now, why would anyone want to continue using a Chameleon module by this point? Simple, to make it more difficult to target your weapons. The simple property of being able to continue using the Chameleon module in the heat of battle would enable a new & huge variety of crafts that don’t really need to hide their weapons so much anymore. Heated parts would still visibly glow a hot red even while the rest of the craft remains invisible, so this could be another way to reveal the shape of an invisible craft (especially when fire puddles & the Trombone would highlight the entire vehicle).
As a side-effect, this would buff missiles quite a bit, but it’d also open the door for new defensive modules such as flares, chaff, or even a module w/ the Griffon’s perk (limited to itself, however).