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Because they want Yuuya to pilot the "TEST" model as an outsider to get another take on it since he has extensive training when it comes to simulation work. They aren't going to improve the training model that he was useing which as been in production for years so him pointing its faults in meaningless since he's only it it so he can learn to pilot a Japanese TSF so he can give a non-bias review of the Test Model and what improvements it could use.
Yuuya has shown that he's extremely bias and if they just put him in the test model(without him understanding the Japanese style) he would disregard anything good about it(which is not what the Japanese want to hear nor the UN) and demand that it be changed into an all American TSF with nothing Japanese in it. Which is stupid since the Japanese Models have already proven just as effective, if not more effective, than the American Models.
From my time in Boot Camp I can honestly say that yes, Yuuya needs to suck it up and do what is expected of him. He didn't tell Yui that he wouldn't follow his orders and told Yui that he has no issue with her, a lie, which means that whatever he gets coming for him is his own fault.
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