You see more seadoos for sale, because they are the hot rod and the people that buy them are the same kind of people that like to have new toys every year or two. I'd seriously recommend staying away from them because they become maintenance intensive with age. Yamis are a solid choice.. Hondas are hard to find because no one sells them locally. However, it is possible to buy 2007 model hondas that are brand new because Honda made more than they could sell for years. A call over to Nashville or Chattanooga might yield a steal on a new ski. Stay away from Polaris.
The ski trailers I have pulled have been extremely easy on the driver. If you have a trailer that is the appropriate size for you ski and it is take care of, you shouldn't have any problems.
I think that covered it all lol. Keep an eye on Ebay and the Bargain Mart, in addition to Craigslist. Fall and spring are the best times to buy, but don't buy anything without test riding it. Its a test ride or no sale.