I have a few, but they would be probably be weird for the gameplay.
1) You always get stronger. Most games have a character go from zero to hero without question, but imagine the oppossite to an extent. Rather than always gain power, you are faced with the dilemma that you may lose power and must plan accordingly. I think in a recent interview one of the concepts for Eternity was that one's power was determined by the completeness of their soul. Imagine if your character's soul(and therefore power) is negatively affected by the game and the choices you make. Perhaps that could be a side quest or even a gameplay mechanic that would make players think before making a rash combat/dialogue decision. It could also be a moral dilemna with a real consequence. For example, you did the "right" thing, but you had to weaken/damage your soul for it.
Ultimately, I think you guys have a very flexible premise to work with. For instance, one could have a passive and constant soul decay system to make the game more challenging, especially if you are inefficient. Additionally, if you are evil you could steal the souls of others to combat the decay, etc.
I am excited to see what Obsidian comes up with.
2) Your character is always pristine or unscathed. No matter the situation, the hero always escapes crippling wounds such as blindness or a missing limb. I realize that there are limitations to this idea, especially for a game that is trying to get the basics down first. For example, it would probably be hard to write for and have combat for a character with no legs. However, I do not think many games or stories explore this aspect much. Part of what I enjoyed about Kreia in Kotor 2 is that even though she was nearly blind and missing a hand, she did not let that stop her.
3) Combat being the only answer. Do not get me wrong, I love combat. However, I do like it when the character is allowed to come up with a nonviolent solution whether by intelegence/charisma or the option is opened by completing a few conditions. Furthermore, I enjoy when that gameplay also has its own rewards whether through xp or certain items. I guess I am imagining Planescape Torment to an extent.
4) Being the student. Plenty of games have your character begin as a student, but few allow you to teach and spread your own philosphy. Kotor 2 gave a nice opportunity to guide your companions' training. If I remember correctly, you could even turn your companions away from the force, which I felt was a fantastic choice to provide.