I would rather any smoking rooms all be on the same floor, and the top floor at that, but I certainly wouldn't want to stay in a non-smoking room on that floor. So then, you'd need to do the entire top floor as smoking.
For the suggestion of making the last rooms on each floor smoking, etc., what if I was assigned the room right next to the smoking one? I certainly couldn't stay in that one if people were actually smoking next door. Smoke does drift.
I also definitely think smoking/non-smoking rooms should be guaranteed. Other hotels can do it, Disney could too. It would be part of the reservation and they know how many they have available. At the point when all that's left is smoking rooms, you then have a choice of taking a smoking room or going somewhere else or changing your dates so what you want is available. I don't see what's so hard about it and was very surprised to find out that my non-smoking room request was simply a request and not guaranteed on my very first stay at WDW. It had me praying that we end up with non-smoking - at the time I had no idea how few rooms there actually were for smoking and upon check-in was told that the only rooms for smoking (this was at CSR) were on the top floor of only one building. I thought then, what a good idea!
I also wanted to mention that the Grand Californian is all non-smoking (as some have already pointed out). Not only that, but the other 2 Disney hotels at
Disneyland, Paradise Pier and Disneyland Hotel are both going to all non-smoking beginning sometime in March, according to a post on the Disneyland board. If that happens then 100% of Disney hotel rooms in CA are non-smoking. If they are doing it there, they may eventually do it here. Or at least to some extent. I've wondered about the possibility of having one resort from each category (value, mod, deluxe, dvc) be a smoking resort and let all the others be non-smoking. What about that idea??? Of course, that may not work as well with DVC since people have home resorts already...