Howdy,
Some of my Wish List for both java and new version. I'm sure some of these have already been mentioned, so I apologize in advance for any duplicates. Some may be best as future plugins:
A slider or some such for game vs real time involving not only day/night cycle but also hunger/thirst. (These, along with real time weather such as MS Flight Sim uses, has been covered, but...)
Boats that can carry cargo. (Water has always been the best logistical method for transporting heavy and bulky goods. Along with many other obvious reasons, most humans live near water. Research suggests that the multi ton stones used to build the Egyptian pyramids were partially transported using the Nile and canals. Etc... ad infinitum.)
Forward movement toggle. (To alleviate hand fatigue when traversing large areas - I have many LONG roads, rivers & canals).
Growing & harvesting grain. (Historically, in Anatolia & later in Mesopotamia for instance, Einkorn wheat was used for many things. One of the oldest recipes discovered in cuneiform, aside from bread, was beer. I don't drink alcohol due to an unfortunate allergy, but it was historically used for trade, and due to poor water quality, beer - as well as wine - was much preferred over tainted drinking water - even into Europe's middle to late ages.)
This was my short list of things that immediately come to mind.
Again I will state that RW is the most enjoyable... I hesitate to call it a "game" as it is so much more. Experimenting with the geometry alone is addictive!
Thank you for reading... 
