I think you should make it so you can't get a part without a unique ability when you defeat a boss, because it's always disappointing when you beat the boss and get a basic connector, or a worse version of a part you have.
Because one time i was the one with the repair ability with its connectors, and i got a basic connector, when in a different one I had both the push-eater, and the bomb eater, making a cannon.
This will add a layer of consistency, knowing that beating a boss will make you stronger.