I don't know if this concept has been suggested before, and if it has, I apologize for the redundancy. But if not, the following is a pretty interesting idea for the next version of GalCiv2:
Why not implement Reverse Engineering as a "research" style action in the next version? Perhaps if you acquire or are given an enemy ship -- or, if you invade and capture a planet with more advanced technology than your own on it -- you can spend your Research bar on "Reverse Engineering" a given piece of technology you've acquired in the process.
Example: Your race does not currently possess Phasor technology. A friendly race gives you one of its ships, which happens to be armed with Phasors. You can choose to Reverse Engineer Phasors instead of researching a given technology on your tree for however many turns it may take to Reverge Engineer the Phasors. Ditto for any given tech you acquire that you haven't yet discovered on your own.
Obviously there should be some balancing put into place to ensure that Reverse Engineering isn't overpowered. Perhaps Reverse Engineering is a very lengthy and time-(or resource-)consuming process. Perhaps you need to research HOW to reverse engineer things before you can even begin to do so. And perhaps you need to reverse engineer something on a planet where you've built the specific facilities. Who knows.