I was thinking, and yes it hurt, before anyone snarks. =P
A few mods have shown that it's possible to tinker with the games main quests without breaking it. So sidequests would also be fair game I imagine.
So... how hard would it be to add 'alternate' quest paths?
For example the suicidal guy in the Shivering Isles. He asks you to help him die; what if there was a Lovers option? Give him a 'reason' to live, that resulted the quest stage being set to completed.
Or, if you were sil