I just bought a Yamaha SX230 from 2008, to replace my Seadoo Sportster 1800. The boat weights twice as much which translates in a much more comfortable ride. There are a few things that seem better made, others where it seems Yamaha tried to reuse existing parts from other products to fit, and it shows. (Throttle Lever Assembly for example, is a total compromise).
It's a unfair comparison mechanically, because the Yamaha is a 4 cycle, Fuel Injected machine, so start up is a piece of cake, and smoke is none existent. I have found that Yamaha owners truly believe Yamaha offers higher quality. My seadoo was very well built, so I have not seen something yet to point to seadoo and compare to how much yamaha did that better in term of quality. On the contrary, I found a few things I wish Yahama did like seadoo (bigger entry ladder, better throttle controls come to mind as "given and expected" in my seadoo that are lacking in the yamaha.
The new (to me) boat is bigger and faster, and seats more people in greater comfort, so for that we are excited.
So far only these 2 things are not favorable. We only have a few hours on it, I thought it was an end of season deal for me, but the weather was good and we have gotten it out quite a few times in the last month or so since we got it.
If you have any specific questions, I'll be happy to answer. I have both boats at the moment and hope to sell the seadoo in the spring.
As a kid my dad has a boat with Twin Yamaha two cycle outboards, and they were quite trouble-free, and it was the brand used by the fishermen in their fishing and tour boats (Enduro 78 and 90 everywhere, pull string) It was then I had some exposure to them and their reputation for quality. (Bikes is also an area they are reputable on)