I have flown the Rotax 912 in the Sport Cruiser and others. It's OK but I don't like the engine. It is my understanding that the 912 performs its best at sea level and "runs out of throttle" at higher altitudes. The 3300 does not. It may produce a better true airspeed at altitude. It will be interesting to see the performance numbers if Jabiru USA does do the conversion. I doubt it will "set the world on fire", but it should be a bit better.
As suggested in an earlier post, I also like the simplicity. Both in the installation and maintenance.
For what it's worth, the 912ULS on my Tornado gives no abnormal trouble at high altitudes. I can still get about 600fpm climb at 10,000' MSL and the EGT's still run in the 1300F range. The Jab will have the same altitude-related power losses since it's also a naturally aspirated engine.
Another disadvantage of the Jab is the high RPM operation, especially with the 2200 - you have to run a pretty small diameter prop to accommodate the higher RPM power output. The effect on climb performance vs. the 912 (with an approx. 2200 rpm prop speed) is going to be obvious (tho it should perform well at speed).
Finally, I havn't found my 912 to be a high maintenance engine. The worst problems I've had on mine have all been routine maintenance issues, the most expensive being the carb rebuild I had to do at 400 hours. You'll have to periodically change the coolant and the rubber hoses - every 5 years if you really want to go by the book, but my hoses are still in good condition at 5 years (so I'm going "on condition").
There's also a lot of mythology about the gearbox which is pretty much just that - horror stories only. The 912ULS gearbox is very strong and has lots of built-in self protection (overload clutch and dog hub system). Vans uses the Sensenitch prop on it also which (I'm pretty sure) meets the MOI requirements of the box. As long your prop isn't a gigantic monster that weighs a ton, the gearbox gives no trouble. So the RV12 installation shouldn't give any trouble.
My 912 has been basically a change-the-oil-and-go-fly engine for the last couple years I've owned it.
So personally, I'm not convinced the Jab would necessarily be a preferable alternative to the 912 on the RV12 airframe. On other planes, yeah, but I don't see any advantage on the 12....
LS