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As much as I would like for that to happen... My guess is that, if what Kishimoto says is true, Yamato will die just because it'll make for a better dramatic element. Killing the guy who can control the Fox's chakra as Naruto summons more tails = berserk fox Naruto with no fail-safe. Plus, IMO the series puts an emphasis on the newer generation... which is why Gaara didn't die (Chiyo instead), Chouji didn't die (Kakashi chose to sacrifice himself... c'mon, who would chose Chouji over Kakashi, seriously?), Jiraiya sacrificed himself to help Naruto/Konoha/new generation, and I don't think Hinata is dead or Sai will die... just because of this.
Unfortunately I agree, I just don't like how that makes the current generation bulletproof. But Yamato makes an even more obvious choice because i'm sure Madara wouldn't be too thrilled to learn the only warrior he ever respected got a watered down clone like that. Still hoping for Sai.