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Re: Atomic 4
I've had both and they're both fine as long as they're in good shape.
Short answer is that there's no reason to rule out an A4. You should make the decision based on the quality of the boat and engine, not on the nameplate in this case. In fact, depending on the model, I might rule out the Yanmar - I had one of those little one-cyl 10hp jobbers and it sucked. Loud and underpowered. A4s can work fine if they've been well-kept and judiciously upgraded. They can be a real pain in the ass if not - but that's true of any engine. Parts are easy to come by and relatively cheap.
Unless one of the engines is in really good (recent rebuild or repower) or really bad (in need of work/rebuild) shape, or if the Yanmar is one of the small 8-10 hp models (not enough for a 28' boat), I'd consider it a tossup and make your decision on other grounds...