I'm not fan of capturing ships. It's unrealistic, can you image Pickard or any other half decent captain to not initiate self destruct sequence when everything is lost? And how are you supposed to use an alien ships if you have no spare parts? And software in the computers that, if nothing else, uses different language? Computers not compatible with your tactical net. Different size of torpedo bays. Steering panels require 7 fingers instead of 5 plus the pilot is supposed to be 50 cm high at most And so on, so on.
It's far easier and more profitable to scrap such captured ship to gather knowledge, not to use it.
Also, even if we ignore realism, I don't think it adds much to the game. I mean, you have choosen a race, you should work around your weakness, not find and steal a ship that complements your setup. Your race does not have cloaking ships, deal with it.