We have Mega-dungeon right? So why don`t make it like stairs to the underworld or something (with own factions, npc, weapons etc).So when you reach it this will affect somehow on the upper-world.(war, smuggling etc)
Proper fighting animation like in NWN (parry etc)
Stronghold with your own army that can become a new side of conflict.
Features with souls like- in memory travels/consumption/ or placement in weapon.
Curses! Curses (like in Baldur's gate) on weapons, armor or something like undroppable sack of potato.
Magic system that requirer sacrifice from you to do high tier spells - like demon`s possession, or health/charisma/etc reduction or some changes in your appearance.Also it would be nice if all spells could interact.Example enemy places something like oil floor spell and you just use your fireball and baam.
In game mini-games (maybe with perk), gambling.
Novice-........-...........- Master system. You can lvl up you`r skills by standard method but title gives you something special (item, skill or just boost).Maybe some Elite classes will fit in this system.
Necromancy - in almost every game necromancy is prohibited.But what if you want to fill your stronghold with undead army?
Low intellect/charisma options.