Oh boy, here we go! You're likely to get strong opinions on both sides.
I own both Rotax and Mercury engined craft so I can speak with experience on both. Here's the short version:
* The Mercury is more reliable and less likely to break, easier to maintain, and costs more to repair.
* The Rotax is less reliable and more likely to break, takes longer and costs more to maintain, and costs less to repair.
Here are the reasons:
* Reliability is primarily driven by how "close to the edge" the engines are run. BRP/Rotax is amazing at extracting the last ounce of performance from a given size engine, but their engines are always running near the limit and that takes its toll on things. Mercury (at least in these V6 2.5L powerplants) runs things more conservatively and therefore things aren't as stressed. Both approaches have their benefits and their supporters and their detractors. Choose which one is more important to YOU.
* Regular maintenance is less costly and time consuming on the Mercury simply because you don't have to do it as often. Annual maintenance is 2-3 hours in your driveway using standard tools and under $100 in parts and chemicals. In contrast, while I'm almost freakishly mental about maintaining my engines I seem to always be troubleshooting and/or replacing something on the Rotaxes. This includes both mechanical and electrical parts. This has led to a standard joke from my wife: "What's wrong with the Rotax THIS time?"
* When something does go wrong, the Mercury parts will cost more. The Rotax engines have a huge aftermarket industry making parts for them. Mercury has some of that, but it's not nearly as big. This may be because more repair parts are NEEDED for Rotax engines vs. Mercury engines, who knows.
Regarding a couple of rumors propagated by the anti-Mercury crowd:
* Mercury has not "orphaned" or "abandoned" the SportJet engines. They are the same exact V6 2.5L powerblock used in countless Mercury outboard engines. All the same tools, training, tests, etc. work on them. If you can find a Mercury shop (and they are far more common than Rotax shops), you've just found a shop that can work on your engine.
* Parts are readily available for the Mercury engines. Since the engines are common to outboards, the parts are often stocked by local Mercury shops on the shelf. Any Mercury dealer can also order parts for you straight from the factory. There are many online sources from whom you can order. And there is a small but solid aftermarket industry for Mercury engines too.
I don't sell anything for either engine. I don't work in the industry. I have nothing to gain regardless of your decision. But I DO own both engine types, I do all of my own maintenance, and I can speak from experience on both. The bottom line is that both are fine choices and your decision should be based on your needs and desires, not on what others try to convince you.
Hope this helps, feel free to ask questions!