Stealth systems tend to require a degree of integration to the design that isn't very modular; if something is to be stealthy, it has to be built from the ground up to take advantage of that stealth. Instead, I'd suggest a stealth system for vees and aerospace that isn't armor and wouldn't require ECM to work. This it would allow them to keep using things like Ferro-Lamellar, Reflective, Hardened armor, etc.
Thus there's design space for an aerospace fighter whose role is reconnaissance and interception, but also room for another of similar weight that is a cheap, robust, all-purpose unit. The heat generated by stealth systems is usually a big burden and means configs have to take that into careful consideration; if the weapon loadout is such that it can't really be used with Stealth active, then any unit using that config is basically paying extra for a system that it can't use.