I feel basically the same as boatermark. Mine had a couple spots on the top of the loader arms and on the back of the mounts. My dealer gave me a touch up pen, kind of like a paint pen, to touch them up with. Can't see them now unless you look for them.
One of the things I like the most about my tractor is all the plastic - fenders, hood, etc.. Paint or not they'll never rust.
I don't expect I will ever wax my tractor. Heck, it barely stays clean long enough to wax it and if I had that much time I wouldn't need a tractor to begin with. However, to each their own, but I would stay away from cleaning waxes regardless.
Keep up with the maintenance schedules 100%, store it out of the sun, and get your work done!