basement bathroom flooring options in old 1929 house
Your options are pretty much infinite. I'd favor gypcrete to raise, level and provide a nice base, then tile. Nothing to rot when the next leak happens (it's a bathroom, there will always be a next leak.) I'd also put radiant floor heat tubing in place in the gypcrete pour, and if there's enough room for sleepers (now), XPS [extruded polystyrene] insulation on top of the concrete floor, under the gypcrete with radiant floor tubing in it. 

If the present floor is rotted, it's probably not cementboard - that doesn't rot.