First off i think water should have some type of depth system to it. At least make it so when you go in it you are swimming and can't do any type of action. Excuse me if that was already suggested before but I think it's a good idea.
Also a weather system would be nice. For now just rain because of all the things it could affect. Like potential flooding or slowing growth of crops because it's cloudy. Maybe refilling wells, all kinds of things.
Now for my main suggestion.
I would like the ability to dig out ponds, maybe a river. I mainly want this this so I can fish close to home. Although it should take a little more work then digging to be able to do this. Maybe in this fashion?
1.You start digging your hole.
2.You fill it with water either from buckets or wait for a rainy day(Related to the above suggestion)
3.Stock it with fish. You would have to fish at an existing source and put the fish in a bucket full of water.(They would just die by the time you got back home otherwise.)
4.Wait a few in game days for the fish to fill up the pond and you have yourself a fishing hole.