I'm not saying the mechanical injection is not preferable on a boat. But saying common rail was developed just to satisfy emission regulations is not true. It was obviously a added bonus that should be cared for if not for our children, but the efficiency, smoothness and power delivery of a modern common rail diesel is so much better then the classic stuff. Especially if you go into turbo-diesel territory.
So in a car its vastly preferably over the old technology. But I do agree, for a boat much less so. But keep in mind the following, there are still people that say a engine has no place on a sailing yacht and you should handle everything with your sails. I'm not one of them but my point is that what now is seen as normal used to be exotic and failure prone. Fact is that a huge number of boats use common rail now and it's not like they are all failing because of whatever.
My point is that when deciding for a new engine, look at the full package and decide on what you feel is important to you. I know there is one Yanmar engine where for many boats it is close to impossible to change the impeller as it sits on the other end of the engine. So if you are in the middle of wherever and need to change a failing impeller you will not be a happy camper. That does not make Yanmar a bad engine. They have a well deserved good reputation.
My own D3-110 has it flaws but I can't complain about the smoothness, efficiency and quietness of this engine. Thanks to being common rail.