One of the main plot quests also has a situation where you have to choose who to help. Unfortunately you are right, these choices can influence experience points, reputation and quest rewards, but do not have a fundamental impact on the story.
The shrine of good and evil has a random effect, though it may be influenced by level or reputation, etc. I saved before talking to it, and could re-load until I got a +5 bonus to the stat of my choice.
