I've spent a lot of time on a Rotax and they have treated me well!! I've got a 94 that runs like a champ. Also, if you ever decide that you want a ski that will jump, other than a stand up, then you better go mid-90's rotax. All of these other heavy tug boats have great power and speed but good luck ever getting one airborne.
I've spent most of my life around Rotax engines and their reliability has always been very questionable. From Ski-doo's (snowmobiles) in Canada to jet-ski's/jetboat's in SC, I've never owned one that was reliable long term.
The last one I owned was a 97 Sea-Doo Speedster that I bought in 99. In 2001 the starboard engine gave out after sounding like crap 'forever'. I ordered a rebuilt, and put it in myself. After the old one was out, I decided to remove the crank cover. All the bearings came dumping out, some were the size of small marbles, some were the size of a large grains of sand, and some were diamond shaped, but none of them were the same size.
I'll never own a Rotax engine ever again. Period. If you want to, that's your choice.
JP