For a lot of rouges and other characters a big part of their skillset involves sneaking, pickpocketing and theft. Many games have implemented this in some form or another to varing degrees of success. I am in the middle of a Pillars of Eternity 2 playthrough and the disappointing pickpocketing mechanic has got my think about what could be done to improve on it. I don't know if the developers look at the posts here, but maybe if they do they might find some good ideas the could try.
Sneaking up to a npc, accessing their inventory and just taking what you want is kinda boring. I did like in DoS2 how they would notice something missing quickly and go to the pc and check. This was definitely abuseable with the magic pockets thing but it was a good step in the right direction.
If you get caught sneaking in shops/sensitive areas they should become suspicious or kick you outside. Maybe have a speech check to mitigate this.
A burglary spree should cause guards to patrol more and people to get on edge, locking away or possibly hiding their valuables. Stolen merchandise should have to be sold through a fence at a lower rate to avoid getting caught, or again have a bluff check involved to convince someone it is not stolen.
Implementing disguises would be cool in general.
The Thieves guild should not be happy without getting a cut.
Assassin's should have more options to poison someone in secret. I don't know if this is possible though since it's doubtful npcs will sleep or eat since there isn't going to be a day/night cycle.
Any other ideas?