My opinion as a UK jetski engineer after riding all 3: (April 2009)
Taking all 3 out in good sized chop, I have to say these are all big heavy machines compared to days of old and 2 strokes, but the manufacturers are combating this ride feel with technology and pure grunt power.
The GTX iS with the latest whole top half deck now with suspension and a braking system is packed with technology, the hull is also new with additional chines. All this makes for a more comfortable ride and ultimately faster cruise speed in chop, I managed 63mph on its gps speedo, apparently good for 67mph on flat water (65mph in USA). This compares to 57mph I managed in the same chop at full throttle on the RXT-X that seemed to be in the air more than in the water. Therefore showing some improvement in chop riding. I also tried the new brake feature, this does slow rapidly but you do get soaked doing it! The other thing I found when performing tight turns in the chop was that the hull seemed to absorb the worst of it, where I was slung around on the X. Ultimately though I found this craft to be a cruiser for ride experience, The RXT-X was more ballistic out of the hole, felt more grunty and aggressive with its identical 255hp engine, probably due to weight and for me personally preferred the more sporty feel over the cruiser feel of the GTX iS.
The FZR was tested 2 weeks earlier in a different area so cannot be likened directly or same choppiness. However, the sea state was choppy and probably similar. This machine is apparently not as powerful as the Seadoo's with its SHO engine but the hull has been lightened from its predecessor by 25% and being a Yamaha was great in the chop, as they are well known for, therefore the pump stayed loaded longer, keeping the power on. It was not quite as aggressive as the RXT-X but felt sportier and quicker than the more powerful GTX iS. The ride felt a lot lighter than it was, and really enjoyable to throw around.
All round I prefer the FZR, as it ticks boxes in sportiness, cruising, acceleration, fun, looks and comfort, great all-rounder. I would add that I am traditionally a Seadoo man, always prefered them but the FZR is in danger of changing that! It is the 'fun factor' that did it for me as the iS didn't quite have that and the RXT-x, although more aggressive wasn't nearly as good in chop and was out of the water half the time.
Hats off to the R&D guys for bringing out new technology!