That was rather vague.
Mostly the tree choices. When it is the colony events, I feel compelled to consider the positive and negatives vs the morality of the choice. When you think about it, that is the way it works in real life. What are you willing to do (or not do) to get the great deal.
I can understand the penalties in the colonizing events, but when you are in the tree the good or bad choices have already been made. I would prefer that tree choices be positive except for some logical, but moderate penalties to approval and influence. Some of the income penalties seem a bit Draconian. There are so many ways to make money, it doesn't make sense to penalize income for moral choices. I can understand a 1 time hit for choosing police state but after that, money penalties should be few and far between, particularly for survivalist.
I have also wondered about the initial building choices being given at the beginning. I can't recall the names but there is a military choice, a research related choice and a wealth choice. Doesn't picking one over the others put you in a certain camp right away. If it is possible it seems that one of the building should be awarded later in the game based on your colonization/event choices up to that point, say turn 100 for instance. As it is, I am always going to pick the money choice (Congress something ?), since I always am always double negative in trade and popularity to allow other trait choices. This is also the reason I am sensitive to money penalties.
BTW I miss the tree choice that increased the effective range of star bases. Maybe you could get that one back in somewhere.