I believe you can trace back most permanent events on planets when you check the 'details' tab on your colony view. Bonuses for research and production are stored there. Keep in mind that economic buildings and capitals also put their bonuses there so don't be fooled by those.
I can see why people feel the 'Good' guys are getting a raw deal, most, if not all the choices they make affect their empire adversely. On the other hand, the defensive techs you can research when you're Good also bestow permanent effects on your ships. The best aspect of being Good, however, is knowing you are Good. It's supposed to give that warm and fuzzy feeling of contentment.
Being Good is all about sacrificing a potential benefit for yourself to benefit others. If that didn't apply, Good would lose a lot of its meaning in my humble opinion. So in short, the choices for Good should hurt you to some degree but the end result of choosing your alignment might then perhaps yield some added (long-term) benefits.
My only real quarrel with alignment is that the game views choices from a third person perspective. Suppose you see yourself as a superior being and, incidentally, all others as various forms of semi-intelligent creatures. Moral choices such as stealing underwater cities wouldn't be much of a problem: you want it, they have it, you take it. You're evil.
But what if you discover those research pods? You don't want to harm your own populace so you leave them. And lo and behold, you're good.
I've used this approach a few times and I've been Good, Neutral and Evil over different games. I feel the choices you are given are more attuned to whether or not you are considerate of the costs others bear for your benefits, regardless of who those others are.
