Did you watch Firefly? Right from the first episode they clearly had plans for where that story was headed, they just never know how many episodes they have to get there.
I did watch Firefly, and enjoyed it very much. Yes, Whedon probably had some details worked out, like the origin of the Reavers etc., and the general direction of the first season. But you can't tell me he had planned through 10 seasons already. That's ridiculous.
Serenity was an incredible opportunity and Whedon didn't waste it.
Depends on how you look at it. The movie certainly was a gift, but I'm not happy with some of the story choices it made. It kind of wasted the potential of the character of Book. Which was later explored in comics (there are several Firefly comics, I haven't kept up with them, though).
So, this comparison isn't really good. Firefly was a TV show. It wasn't resurrected in the same medium. It got a movie. And that wasn't even the end. It got several comics...
Shenmue on the other hand was a game series and it does get a direct sequel in the same medium.
How about another bad comparison: George R.R. Martin's "A Song of Ice and Fire". Originally planned to be a trilogy. But grew to 7 books. Might even be 8. Only 5 have been released so far. And there certainly are people who wish that the story would be wrapped up with the upcoming book 6, because of the author's glacial pace. After all, he might die (god forbid) before he'll be able to finish the story.
He has a great answer to those concerns.
There's no reason Suzuki could not have compressed the story into something quite exceptional and satisfying for 3.
Oh yes, there is: money. The game appears to be "underfunded" as is, no need to make things worse by cramming more story into it. Also, what you consider to be "trimmable fat" in a story, others might think of as the best part... I don't see how a premature ending of any story could ever be exceptional and satisfying.