There are no major issues on any of the Yamaha 4 strokes. There have been minor recalls to some models, but nothing major, and all repairs are covered regardless if you are the original owner or not, so even if you buy a used ski that has not had the recall you could take it to a dealer and have it done for free.
The only thing that comes to mind is a "bucking" issue reported by a few owners with the 2009 model FZS/FZR. This issue was fixed on later models, and can be easily fixed on the 09 with a new intake grate.
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2008 Yamaha FX HO Cruiser
2010 Hurricane Sundeck 2100
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