We left the original bus floor (ours is over metal, not plywood), took out the metal strips on either side of the aisle to make it flat, and laid down foam underlayment/moisture barrier, then put cheapo $1/sq ft laminate wood flooring on top. The kitchen and bathroom have a sheet of luan over the foam underlayment, with stick on tiles on top of the plywood. We've been living in it full time since then (June 2014) and have traveled over 8000 miles in all kinds of weather and washboard dirt roads, sand, mud, and I-don't-know-what-else since then, and it's holding up great. Although if you let a puddle of water sit on the floor for too long I could see how it might soak into the seams of the laminate. We didn't fasten the floor down at all; we just built all our furniture right on top of it and screwed the furniture in. It doesn't move at all.
If I had to do it again and I had the head room (I'm short, but not everyone is...) I'd put foam board insulation under it first.
My build thread:http://www.skoolie.net/forums/f11/build-thread-for-haulin-oats-and-goats-11237.html#post113500
A gal, a guy, three cats, two dogs, one rabbit, and one goat, traveling the country together.