I was thinking the same thing a while back, for some reason I assumed there was going to be rain in the game. Cloud cover would be a nice feature, and sometimes the occasional storm cloud flying overhead with it's thunder and rain.

Definitely need this.  Weather makes every game better (Stalker is a great example of this).  It goes a long way in setting the mood.  I also would like to see seasonal changes on the map at some point.  For example, autumn would make the trees change color and maybe increase the chance of rain.  Also, autumn would be harvesting season, so maybe their could be a harvest bonus or something.  And so on.  The seasons were so important to the medieval world, I would love to see them implemented at some point.  After all...winter is coming. 

Maybe it something we can mod in fairly easily. With the ability to raise and lower land it would be cool to have terrain affected by weather patterns Alpha Centuri style.

You've got an enemy living to the East? Raise a mountain between you and him so clouds build up on your side making the land more fertile while his dries out and becomes desert. It's not a violation of the non aggression treaty.