Chef,
Good question......I would say a lot depends on the support of the manufacturer, parts availability, and comparative engine displacement/HP. Will the replacement engine fit onto the existing engine support box without too much alteration. Prop shaft sizing? Will you need a new prop? One important issue: is the engine you're looking at designed for the new ultra-low sulphur diesel? This is important because the older engines rely on the sulphur as a lubricant and the ultra-low sulpher fuels can damage seals etc. If it weren't for this issue, I would consider a re-build as to keep the replacement costs down. The other consideration that I would have is more philosophical.....is it made (or at least assembeled) in the USA thus supporting jobs here.
Let us know which one you're going with
Tom