I agree with YamaDoo. I'd go with the non-turbo Honda. Most problems you see are with the turbo on the Hondas. The non-turbo model is a pretty solid performer. It has a sporty ride, not super fast, but not a bad family machine. It will be more reliable, but keep in mind that Honda is out of the ski business for now. They haven't produced a ski since 2009, and many Honda PWC dealerships and their mechanics are getting hard to find if you do have a problem........one of the reasons that used Honda skis are selling for such low prices.
The Yamaha XLT 1200 is a 2 stroke, so you have to add oil, and may have an oil pump and lines to worry about, plus cleaning carbs periodically, catalyic converter failure problems, power valve failure problems...........etc.. For new owners, I'd recommend avoiding 2 stroke skis, unless you are good with a wrench.