Waiting for the shops to open or for key NPCs to get out of bed is annoying, though actually I find a schedule helps my roleplaying: I figure that my character also needs a rest occasionally and can't do 24-hour questing. In games with day/night schedules, if possible I tend to make the nights really dark, unless the weather's clear and it's a full moon (actually I forget if the moon(s) ever make a difference, but the weather certainly does). I admit it's sometimes annoying wandering around Cyrodiil or the Capital Wasteland not being able to see a hand in front of me and hearing various growling noises fairly close by! Especially as bad planning means I can inadvertently get caught by the sunset when I'm away from a settlement, meaning stumbling through the dark as I prefer not to fast-travel either.
I agree about the rain, though. I start to feel persecuted when even the weather in my games has it in for me!
What I like about day-night in Witcher 3 is the change in atmosphere it brings. That's it, really. In W3, the day-night schedules do not change simply because the sun goes down. Things do however manage to look much different at night--and I think that alone lends them credibility. And as well, in W3 there are several scenarios that can only be accomplished @ night. I don't think Larian would have to carry it any further than that. These are fantasy games in fantasy worlds and nobody expects an entirely different world when the sun drops below the horizon--no need at all for a "night-shift" game.
I mention W3 also because you mention the weather--and I agree with you that it is often irritating. However, in W3 they've managed to make even inclement weather highly entertaining...like when the dark/black clouds roll in and the wind whips up...I often stop to just watch...;)
