Some of these may have already been suggested but I haven't seen a lot of them
This is my personal suggestion list
Running over creatures with a vehicle kills them (or make it an option)
Actual doors and gates (automated option too)
Power lines, conveyors and buildings will automatically cut a hole in walls/floors
Selectable character gender
The winch on vehicles has uses IE: Pulling vehicle out of water or from being stuck, pulling down trees you can't run over, pulling other vehicles
Trailer that attaches to tractors and trucks
Conveyor belts and power lines won't clip through almost anything (or make it an option)
Some of these suggestions can possibly be implemented by way of making difficulties