I would paint the floor and then fit it with some lino - preferably so it just goes slightly up at the edges (and is fastened to stop it being chewed), so it can be disinfected properly. Bare wood is very difficult to clean properly. Rabbits are quite prone to the EC parasite which is shed in the urine of an infected animal. Urine soaks into unpainted wood. Anything that makes it easier to disinfect when needed is a bonus, and is much easier to design in with new housing. It also makes daily spot-cleaning much easier.
Painting the walls will also make them easier to wipe down, particularly in the splash zone (bottom 2' or so). I have used leftover household emulsion paint for this before. It doesn't have to cost much, and doesn't take long to do, but the benefits are definitely worth it. You can also get creative with the inside, depending on what paint you have - the rabbits won't mind the new artwork.