In my opinion displacement is better than a smaller motor putting out more horsepower. The way you need to look at it a smaller motor needs to work harder to put out more power than a bigger motor so in turn that wears the motor out quicker.
Seadoo's engine has been tried and tested for years and is locked in. More displacement just means a bigger, heavier and in this case, a less powerful and less power efficient engine. If you go with the new SHO you have to take the risk of using an engine that has just come out on the market. While the chances of it crashing and burning are slim and none, you know what you are getting with the RXT. If you can fork out a bit more then we are talking RXT-X range, which beats the SHO anyday, hands down (using the same engine as the RXT with an added external intercooler). I can vouch for the RXT-X, a bud of mine went out to Palm Desert, CA where he got a chance to test both the RXP-X and the RXT-X. All he had to say was that it was the fastest stock machine he's ever been on.