I saw some cool things with the weather but I thought I might add a few things. One cool thing would be in a thunder storm there is a chance of a tornado forming which can destroy any structure consisted of sand, clay, dirt, or wood. Also if a player runs into a tornado they can take damage by being within a 3 block distance of it by getting hit from blocks picked up. Animals and monsters can also be picked up the tornado. A second idea I would have is that when it rains all open flames such as torches not covered by a block not on fire. As well during the rain storm puddle can form on the ground which would be the same as placing a water block on the ground.
Best Texture pack eva!
2) Maybe...
3) No. If anything, it should be a simple (temporary!) puddle with a little splash effect when walked through.