i have not owned a rotax motor but i do know they are quality, reliable motors. however if i had the choice i would want one mercury in my boat for multiple reasons.
1. power. yes the supercharged rotaxs may have more hp but in torque there is no comparison. and torque plays a huge roll in jet boats, especially with how big the boats are getting.
2. maintenance. two motors and pumps = twice the maintenance and twice the possibility for something to go wrong.
3. parts/dealer availability. atleast in my area, and im pretty sure its the same everywhere, theres probably 6 mercury dealers to one sea-doo dealer. you can go to a merc dealer and they'd happily work on a 40 year old mercury, no such thing as poor support for the mercurys. plus i can find quicksilver oils/lubes in any local hardware store. cant find that with rotax stuff.
4. fuel consumption. theres no way two motors that are spinning higher rpms are burning less fuel than one motor. ive never had a reason to complain about the fuel consumption from my sport jets.
having said that i dont think i would complain much about have two new rotaxs in my boat. maybe i will in the future. but if i could get two mercury 240s or 250s, now we'd be talking!