I think the side quest choices in RPG are too easy to make. There are no occasion where you really have to decide whether to get involved at all.
1. The cost for good-guy choice is too low.
It's usually like this:
NPC: "Thanks for saving my son, please, take this." *offers to give $1* (when the player is already a millionaire)
Player: [Good karma response] *refuse the $1*
NPC: "Oh my god you are the single most best bestest person in the world, hope of humanity!!!1!!1!1111!"
[Karma gained]
The cost is so negligible, there is not really any sacrifice, and so there is no need to decide whether to help or not.
Instead, what if:
"You want to free this slave? Why don't you pay [an amount scaled to the player's wealth, perhaps even more than it] for her contract?"
"The sentence for this street urchin is his left hand, if you want him released, then part with your hand in place of him" And from then on, you can't equip with your left hand nor use two-handed equipment...etc
"My guy saw that [important unique weapon owned by player] of yours when you entered the town, if the life of this peasant is so important to you, then let's trade"
and so on... are you willing to help everyone?
2. The consequence of bad-guy choice is too low
It's usually like this:
Pissing off the local crime lord who have been terrorizing the town for years as a newcomer? It's ok, they will forget everything once you step out of this room.
Instead, what if:
You are thoroughly beaten and have some items taken off.
Some merchants would be scared to trade with you lest they enrage the crime lord.
You would be hunted repeatedly and have to sneak around the town to avoid them.
and so on... are you willing to confront everything?
3. The outcome is too predictable.
It's always good choice = "oh thank you hero, here's a gift"
why is no one in the ghetto ****hole city-of-vice town trying to scam this newcomer at all, who is running around asking everyone basic question like a tourist?
there should be way more quests that the npc turns out to be just playing you for fool, ether outright taunting you after receiving your help and running away letting you chase them, or there is some subtle evidence that can be discovered and to confront the npc with.
For replayability's sake perhaps the npc's integrity should even be randomly determined at the start of the playthrough.
and so on... are you willing to get involved with everyone?
I think if these are addressed, then there will be much more sense of accomplishment when your character sticks to his principle, be it good, bad, greedy, pragmatic, insane. It's also much more memorable when you can't automatically accept everything and have to think about it (and when you are trolled by npc, )