Big Boss made Outer Heaven to create place where soldiers aren't used as tools by their countries, and all that jazz, hence MGS3 being him witnessing him and the Boss being used as tools by their country. How much he respected the Boss in spite of her letting herself be used as tool changed between MGS3, PO and PW, whether she let that happen at all (if she decided to **** all what her mission is concerned so she can fight her student in earnest then that would be no) is left up to you.
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When you've got a pretty-boy monkey on your back constantly calling you a puppet, you hardly want to seem like you're happy to be used. - DSakaCharanJ