Mercury engines are well known, well serviced, very popular...
I don't know why people are saying that the Mercury powered Seadoos are a bad idea. I have both kinds of engines (a Mercury SportJet 240EFI engine in my 2001 Challenger 2000, and two Rotax 787 engines in my two jetskis), and maintain and service all three myself, so I believe I can speak without bias.
I am just now completing a mini-overhaul on the Mercury engine after about nine years of life and hundreds of hours of use. Not because anything was wrong with it, but because I like to stay ahead of maintenance and do it on my schedule. Parts for this engine and jetdrive are EASY to find. There are dozens of online sources, any Mercury dealer can and will order them, and even eBay has lots of parts available both new and used.
Why? Because the SportJet engines are really just standard Mercury outboard engines used on an inboard boat. That V6 engine has been made by Mercury for many, many years. Take it to any Mercury shop anywhere - and there are FAR more Mercury shops than BRP/Seadoo/Rotax shops! - and they will instantly recognize the engine because it is exactly like their outboards. It's the same engine. Any certified Mercury shop will be able to work on your engine. All the tools are the same, all the diagnostic tests are the same, the DDT (fancy engine tester) plugs right into the same connector... it's all identical.
Don't fall into the trap of believing that your boat and your engine have to be made by the same company. That's common for jetskis. It's unusual for real boats. Ever heard of an engine made by Mastercraft? Tige? Supra? Nope. They all buy from ENGINE manufacturers like Mercury, Volvo, and Cummins. (That's how aircraft makers like Boeing, Airbus, Cessna, and Robinson do it, too - they focus on the vessel and buy engines from companies like GE, Rolls Royce, Garrett, and Lycoming.)
I own, use, and maintain both kinds of engines. Here's a synopsis of what I've found. The Rotax engines are simpler in design and the parts can be cheaper. However, they fail more often and require more work to keep running. I've probably spent 3-4X the clock time and money maintaining and repairing my two Rotax engines as I have my one Mercury SportJet, and I've owned the Mercury more than twice as long and it sees probably 3-4X the hours of operation.
There's a lot of good things to be said about the Rotax engines. But in my educated opinion, the Mercury engines are superior for actual BOAT applications. For jetskis, the Rotax engines are small, light, simple, and reasonably reliable. But if you're driving a vessel large enough to hold a Mercury engine, you're better off having one.
Again, I have no bias in this discussion. I don't work for either company, I don't sell anything related to boating, etc. But I do own and work on both kinds of engines and can speak from years of personal experience. With all due respect, the earlier respondents are incorrect in their comments regarding the Mercury powerplants.
If you're still unsure, do your own research... call a few boat shops and see which brand is more popular... see how many can get parts for, and know how to work on, V6 Mercury engines as compared with Rotax engines. What you'll find is that Rotax will be serviced by a few jetski/motorcycle shops, while Mercury will be serviced by tons of real boat dealers and marine engine shops. Then you can make an informed decision.
Report back, and good luck!