So I think these ideas would make a great mod which might become possible after the GECK is released, but would be great if the devs took the time to get this into the game proper.

1) Weather-based behavior: When there is a thunderstorm or radstorm, the NPC just mill about as if nothing were going on. It could be causing +5 radiation but an old woman is still calmly stirring her pot in Goodneighbor. I would expect people to run to find shelter.

2) Day/night cycles: Everyone stays in their pre-assigned locations no matter what time of day it is. Yes, there are a few people that go to sleep like in Diamond City, but there are still tons of NPC's that just continue to mill about as if it were broad daylight.

3) Day/night cycles for lighting: Usually in cities and towns most of the town's lights go out at night. It would be cool if towns received a day/night cycle where most of the lights go out from about 11pm till 5pm the next day. In vaults, it would go to subdued "night" lighting, and only a few people might be seen out in the halls like a night janitor sweeping or something.

4) Vendors give you different responses depending on when you last saw them, if you purchased from them before, etc. Like seeing an old friend you haven't seen in a long time.