If I remember correctly, BG2 has a small quest requiring investigation on some murder cases. In order to have more interesting quests, could we have something like this.
There could be a series of preliminary small quests given by a guild or gathering of detectives. Undertaking these quests could improve one's awareness and detective skills. After undertaking a series of smaller quests, the PC could stumble onto the main quest.
This could be an overarching plot, such a a secret clut ala Cthulhu that is trying to revive their Dead God by performing a series of macabre rituals through certain locations empowered by lay-lines (i.e. magically empowered locations). The local authorities in each of these regions are stumped as they are working individually.
Throughout his adventures, the PC will stumble onto the aftermath of these bizzare rituals. If he is intelligent enough or has a companion who is, he will detect similarities between each of these rituals. E.g. the murder victims were killed the same type of weapon, death occured during full moon etc.
This may set him off to investigate the individuals in town and uncover the conspiracy taking place amongst the cultist. The finale may involve the PC either:
1. Exposing and eliminating the cult
2. Threatening the cult and obtain bribes to keep his mouth shut.
3. Joining the cult and fusing his soul with the Elder God for awesome powers in the current gameplay, at the cost of permanently damning his soul...