I'm
really not a fan of random chance in games, so I'd be reluctant to add failure rates.
What if the factory required multiple hulls to analyze before it can decipher the blueprints? Say one hull for fighters/frigates, two for destroyers/cruisers, three for capitals? It would make adding high-tier ships to the factory a much larger sacrifice than it is currently, but you could still have a healthy supply of low-level ships.
And I think if you somehow manage to capture/purchase three Paragons and are willing to give them up, you
deserve to have a steady supply later on.