Oh I have so many ideas
The most important thing for me is the attitude in writing storyline and questlines. You have to at every point of a story ask yourself what would player want to do in given situation. Or even better, ask some people what would they do and take note of every answer and implement best of them into a game. It seems hard and expensive but that's the way best cRPGs do it. Start from making everyone mortal.
Example:
1. I got a quest to rob a bank
2. I can:
a) Do it myself by taking hostages or simply shooting everyone or do it by preping and gathering info and then sneaking in acording to your master plan
b) do it as a leader of a team of mercs in same few ways
c) Kidnap thief or thieves attach bomb collars to them and blackmail them into executing your plan
d) Mind control some people
(mind control device and collar blue prints being obtained in some other questline as a reward for being egocentric)
3. I can choose to kill my helpers
4. Multiple endings of this quest with different rewards like reps with different factions depending on my approach.
5. Few acknowledgements in dialogs and in the end game.