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The issue isn't that they switched plots. It's that they established a plot, and then introduced a plot that was related to the plot initially established, but in actuality had little to no direct relevance.
Let me explain: They started with Yui in Japan fighting the BETA. They switched to Alaska with a testing program for creating better TSFs to "fight the BETA." The issue is that the TSF development is basically not related to the BETA at all, and all of the governments of the world are still running around making secret weapons to carry on a ridiculous Cold War scenario, almost oblivious to the whole man-eating aliens thing.
I say this often about Muv-Luv, but they could have pursued that Blue Gender sort of idea in a more 08th MS Team format as was mentioned before. I would have loved to have watched them done some meaningful development of new TSFs whilst fighting off aliens. It's a hell of a lot more entertaining than sitting there saying: "Am I the only one who still cares about the whole aliens thing?"
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