Admiral: Right now, you never have to research any spacedock ships (beside parasites (well, and scouts)) because you can just steal them. My suggestion is purely a limitation, so I don't see why this feature would change your research habits.
I see the purpose of parasites to steal enemy ships, and nerfing them such that they can't do it beyond unit caps (or not far beyond unit caps, as Rev has suggested) seems reasonable considering that right now you can get endless armies of what sounds like game-breaking size. In my last game, I'd built Mark I-IV of all 10 available spacedock ships (parasites included) and was pumping out starships, all supported by two mark II reactors per world I owned. It was pretty tight, but I was getting by, and my fleet was absolutely massive and could tackle anything, and this was without using parasites that much (just as a normal unit and to capture mark III engineers). Throwing nearly 90,000 more energy on each world..frankly, I can't imagine a fleet that size being balanced in any way. Furthermore, unit caps exist partially to keep you from creating fleets of a single ship that you consider the best (without unit caps, my fleet would be thousands of deflector drones and snipers, with some fighters/bombers along for the ride to cover ships the others can't kill) and to keep fleets reasonably sized. In setting terms, it also makes sense as the number of ships of a type that you can keep serviced.
The big plus, in my opinion, to parasites is getting ships from the AI that you can't get otherwise, in addition to getting ships for free. Being able to use them to ignore any sort of unit cap is much akin to ships at docks not having a unit cap, allowing you to build as much as you want. The mark III reactor should make energy management trivial in most any game, but you're consistently on the brink even with that and the others, which really says to me that these things are way overpowered (I argue game-breaking. With unlimited ships, how much strategy is left in the game?). I feel limiting the number of ships you can capture based in some way on that ship type's cap, as well as possibly reducing or eliminating previous nerfs to parasites (cost and build time), would probably be a reasonable way to go.