I'd do it a little differently. Instead of having a class of "cloaking devices" that you can put on your ships, make it a line of techs for stealth technologies and electroninc warfare. Initial devices would be simple sensor jammers and such, while the more powerful instances would be outright cloaking devices (or perhaps even devices which shift a ship into an alternate dimension!)
Every component that this technology yields will becomes steadily more powerful. +1 stealth would allow a ship to not appear on the outer edge of another ship's radar, +2 further decreasing that distance, etc. You'd eventually be able to yield a ship entirely invisible by exceeding the sensor range with stealth components. Countering it would be a matter of increasing the sensors on your ships.
Perhaps an additional bonus could be given to a ship that was rendered invisible to sensors, on par with the Arcean first strike ability.
I agree with this. Stealth tech should be another defensive branch, except it's not a normal defense that counters a specific type of weapon. Instead, it counters sensors.
IMO, stealth ships should not have a first strike ability since if it gets attacked, it probably has been seen, and that means it's stealth has been overcome.
Instead, stealth tech should decrease enemy attack rolls by 5% for every point of stealthiness. That way, if a ship fires at a target who has a stealth rating of 5, that ship can only roll it's weapon from 0% to 75% of it's maximum attack power.
The stealth tech tree could look like this:
Jammers -> Absorption Materials -> Stealth Hulls -> Deception -> Cloaks
With various, slight modifications for the different races(From TA, races will have unique tech trees). Jammers would be simple components that you put on ships to add stealth points. Absorption Materials would be smaller and more potent but the same.
Stealth Hulls would allow for the building of new, stealthy hull designs that sacrifice a bit of hull space for high levels of stealthiness.
Deception would be in the form of small and powerful components that, if the ship is detected, would show the ship to be something it isn't. For example, a transport with Deception components would appear to an enemy as being a scout, or something of the sort. Only ships using a Survey Module would be able to tell what a deceptive ship actually is.
Cloaks would be extremely expensive, very small components that add high stealth rating to ships as well as make them deceptive.