Off the top of my head, among the thousands of commits since 3.0:
- real interfaces for all NPCs
- a flexible quest system with a GUI editor instead of using Python to code the quests, also support for multi-multi-part quests (essentially any level of multi-) and repeatable (eg, daily) quests
- 3D map system (try going upstairs in some building and looking out of a window -- you will see the outside in real-time)
- 3D sounds and ambient sound effects
- new combat system (can only use one kind of a skill now instead of spam using spells, archery and melee all at once)
- new party system with a widget that updates hp/mana bars of party members in real time
- forced combat mode that will allow you to attack friendlies (press shift+c to toggle on/off)
- factions (if you attack an NPC in Brynknot for example, the guards will run to the NPC's aid, and if you kill the NPC you will get a bounty on your head, which can be cleared for a price by talking to a guard [who will stop you anyway if you approach with a bounty], or going to the Thieves Guild in Asteria to get it cleared for a lower price)
- wizards tower remake
And many others beside that I can't remember...
Speaking of Thieves Guild, this makes me think there could be a guild that specialize in killing people. For instance if they could give you jobs, or hits, so you can make some money and you have to kill NPCs that they give you a hit for. Ofc you will need ways to do this stealthily or you will get a hefty bounty every time you kill.
Edit: Same goes for Thieves Guild. I managed to find it in Asteria. They could also offer jobs to steal things from NPCs which could give way to a new skill either called pickpocketing or thieving. Both Guilds could make way for a stealth skill as well.