I felt like the ending, the true ending, was Kojima's way of saying that you, the player, are now Big Boss. It's like Big Boss said in the tape, "Thanks to you I left my mark. You have too. You've written your own history. You're your own man. I'm Big Boss, and you are too. He's the two of us together. Where we are today, we built it. This story, this legend...is our's. From here on out, you're Big Boss." The medic was supposed to be you, the player, someone who trusted and observed Big Boss, yet at the same time someone Big Boss also trusted. The realization that you weren't Big Boss himself from the start, that empty feeling, is the realization that the man you trusted had betrayed you. He molded you into his phantom to further his own legend. Now, at the end of it all you are left with a choice: Embrace your new identity as the phantom of Big Boss, or break the mirror and resent it.
Also one thing I will never get is why so many people were obsessed with wanting to rescue Naomi, Grey Fox, Sniper Wolf, etc. in MGS5. I mean for fuck's sake, it would have probably ended up being a fucking fulton mission! We rescue a guy who may or may not be Dr. Madnar, and hell, even that was just a quick fulton. We rescue a ton of people, and hell, maybe Grey Fox gets retconned into being the commander of a unit of African child soldiers, but after getting burned during the making of a Pepsi commercial becomes a white guy, and hence is why he sounds like a black guy that smoked an entire Marlboro factory in the original MGS.