With modern four strokes, inboards really only hold the advantage of price. What happens is when you take an engine with iron manifolds, mate it to an aluminium leg is you create a big battery, which can be hard on aluminium. Yes, you can zinc the hell out of it, but in the end, they all do a pretty good impression of an eroding urinal cake.
There are a myriad of little things to go wrong wtih a stern drive, the engine is usually fine, but I'm willing to bet you go through starters, alternators, etc etc a lot faster then in an outboard. This is because these things are usually sitting in the humid environment of a bilge.
The argument that "If anything goes wrong wtih a car engine, I can fix it" may work in some instances, but the reason most guide/whale boats have outboards is that you are far less likeley to develop problems with an outboard then an inboard. And most modern computer controlled inboards are probably beyond what most guys can tackle anyway, so you get the complexity of a computer controlled engine with the honour of fixing it head-first, upside down in a cramped bilge compartment designed to barley fit the thing, let alone service it.
Talk to someone with 1000 hours on an inboard, and see what they do to it for maintainance. I'll bet a couple sets of risers, gimball boots, altenators and starters will come up in conversation.Then see what someone with 1000 hours on a modern outboard does for service on them. My last four stroke outboard with 600 hours on it never got anything more then plugs and oil.
A couple of guides I run with have over 1600 hours on their four stroke Yam's, and all they have done is impellers (once), and one injector.
Inboards have a good place in freshwater ski boats, where corrosion is not nearly a problem, and the clean transom and weight slightly forward help for the boats intended purpose, that is, pulling a skier.
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