Along the lines of balancing, doesn't the power priority menu help with that? What I mean is cloaking could have priority, then there wouldn't be enough power to spare for weapons systems. If weapons have priority, the stealth drive may not get enough power to keep perma-cloaking.
Also, having multiple reactors is somewhat not ideal, because the chambers need time to have their full effect. If that wasn't much of a problem though, balancing how much power a ship needs to cloak wouldn't be too hard, it would just be a lot of guess and check.
Maybe cloaking could take into account not just mass, but what systems are on the ship and how big they are. It could take more power to hide a ship that uses a lot of power, i.e. if they have massive guns to charge up or a lot of shield to keep up, that's a lot of power being used, which could make the ship harder for its jammers to hide.
That last proposal is just an idea, not something I want to see in game; it would take a while to implement I assume.