Ride them both then decide = most important factor. Where will you ride? The GTX may have an advantage with the closed loop cooling if you are going to be in salt water most of the time........may be a disadvantage if you will be in fresh water, since it is known to have more maintance headaches.
Both fast
Seadoo = more gimicks = more stuff to fail or have problems with (I'd say the brakes are pretty much a sales gimick, and will not be that useful, but the icontrol feature could be nice if you do lots of towing), nice rough water ride
Yamaha = more reliable, really drinks the gas, but uses regular, also good in the rough stuff, also has a cruise control, but not as many features as Seadoo's icontrol.
If top speed is not an issue the 2009 or 2010 FX HO would be a better option over the SHO IMO. It gets much better gas mileage, you don't have the supercharger to worry about, and speed is still plenty fast.