Even my rabbit lived in a crate, not a cage. I just didn't like the idea of him walking on wire all the time.
Sure, the poop goes to the bottom and is separated...but if you clean it out every day like a RESPONSIBLE owner, it's not a problem. Our rabbit, who stayed out most of the time, had a crate filled w/ cedar that we cleaned out EVERY day...never had problems with mess, smell, or anything of the sort.