Seadoo always builds fo the most power and new tech and as we all know with more power comes less reliability. Yamaha builds a true marine engine with sacrificial anodes and coatings to resist corrosion. Yamaha has always put reliability first and performance second.
I personally know two seadoo dealers that are fed up with seadoo reliability. One of them recently dropped seadoo watercraft because they could not keep up with the repairs and warranty work and they were already selling Yamaha's which had very few if any repairs.
The other dealer has been selling Seadoo's since the 90's and stated that the only reason he continues to sell the watercraft is so that he can keep the Can-Am line and if he could he would drop the watercraft immediately due to poor reliability.
Also look and any rental fleets, they are always Yamaha waverunners. There must be a reason because purchase price is the same a seadoo, also look here at the forums and see all the issues with the Superchargers, valves, hull cracking and bubbling and Spark driveshaft failures.