Hey I may be a little late in offering my two cents. But here it is anyway. You can't go wrong with either Seadoo or Yamaha. I personally prefer Seadoo for a few reasons. First is performance my skis run very well and seem to to be faster than like models of Yamahas. I have a 2006 RXT which has a RIVA stage III kit plus some other goodies and is approx 300 hp and runs out out in the high 70's. Best run is 78 mph on gps. My point is being that highly modified it runs as smooth and dependable as any stock ski. I have a GTX 215 that is stock and handles the chop very well.
I have to correct the statement that you have run premium fuel in Seadoos, it is "recommended" but not manditory for optimum performance. When running lower octanes the ECU automatically detects the lower octane and retards the timing to compensate so it will run like skis that don't use premium i.e Yamaha. I have been in the water and low on fuel and ran 89 octane in my modded RXT with no problem.
As far as closed loop cooling goes, it makes sense to me not to run salt water through the engines internals. If you don't flush every time it will corrode. The longer it sits not being flushed the worse the damage is. I can't think of any disadvantage of using it. When it comes to winterizing it does involve a little more smarts to do it. But I do all my own winterizing and it is simple once you understand what to do.
When it comes to seaweed/seagrass if you can't avoid it the best thing to do is nail the throttle so the ;pump will homoginize it. The worst thing to do is to try and tip toe through it, you will clog the pump and overheat the engine and melt any platsitic tubes.
I also was at the Atlantic city Boat show and the only brands there were Seadoo and Yamaha. No Kawasaki dealers at all. That kinda says something.
For my money I will choose Seadoo, but Yamaha would be the next logical choice.
Good luck and happy trails