Although I think it's decently balanced as it is... now that you mention it, it would be interesting to see some occational random rewards for being good even if their effects were minimal. Like maybe another good AI could contact you and commend your actions with a situation or the UP could award you with a gold star to put on your refrigerator. Maybe taking the evil options could occationally have bad side-effects that back fire on you. Oh well, I'm just thinking out loud... er in text...
Kind of on the subject, I would like to re-write a few of the dilemma options. Like finding the high tech ship, why is it neutral to ask them to share some tech with you? I would think something like:
Good, Ask for any information about the vessel they are willing to give (very small bonus)
Neutral, scan the ship w/o permission or plant bugs / surveillance probes or something to spy on it.
Evil would be the same. Jack the ship, torture the crew, etc.