Since you do not want to do this again and you have the hardest work done. I would use 3/4 inch treated ply or marine ply for sub flooring and be sure to screw it down with coated screws. And screw it down every 6 inches
Now, you may not be able to go for 3/4 inch because of height build up. What was the thickness of the stuff you took out?
Remember you have the thickness of the sub floor, the wonder board, the tile. So, what is the height of the comode collar? Do you have a tub in there? Do you have the old sink or cabinet to go back in there?
What I want you to consider is the building up of the height of the floor if something will not go back.
But, do not skimp on this subfloor, this is the very foundation for all to sit. If the tile you say is ceramic, you must, you must have a very stable, no bounce flooring or the ceramic grout will break.
I would if you could go with the first suggestion.