I interpreted this very differently. This is in fact my favourite part of the twist. It's the notion that Big Boss is an idea, a legend that was constructed rather than born. Big Boss the man defeated The Boss in personal combat. Big Boss, the legend of the battlefield is a different entity. This is a theme repeated throughout the series, that image is different to the reality, and that image can be cultivated to suit your career or political needs.The reveal that you're Big Boss' “double” felt very rushed and out of the blue, but most of all, undeserved. You're supposed to believe that your character, someone who was never mentioned before outside of this game's context, is as good as "The Greatest Warrior of the 20th Century”. If it was someone we knew, like Frank Jaeger for example, it could have been a great reveal or at least have a little more gravitas, and the suspension of disbelief wouldn't be ruined since the facial reconstruction technology they have in the game seems to be way more advanced than the one we have in the real world, but as it stands, it falls flat on its face because at no point we have any sort of attachment to the unnamed medic.
On Mother Base, everyone has innate abilities to some degree, but they can all be trained and surpass Venom Snake. However, your actions as Venom - who let's face it, is probably the one you'll end up playing as due to his bionic arm, are actually building towards the legend of Big Boss, driving home how artificial and Machiavellian he is. In general the series plays with the idea of identity and how it can be made and unmade. So I wholly accept and endorse this aspect of the twist.
Going a bit beyond this, Kojima wanted to speak to the player directly. Now this part was a little more hamfisted than the above(that Big Boss is an identity/notion as opposed to a specific person) - but I'm sure we can agree that if it was an established character like Frank Jaeger [Gray Fox, for the uninitiated], it wouldn't have spoken to the player but would have entirely been about MGS lore. The point was that anyone can be Big Boss, the player included. More importantly, it's the point that Big Boss is an ideal, a Platonic form, not a specific person. I feel that's what they were driving at and I like this take a great deal, and I find it concordant with the series' themes.
What annoyed me personally, as expanded on in my review, is all the other plot stuff preceding it. I thought the twist was very nearly the sole decent moment in what was otherwise a boring and very thin plot, completely uninteresting characters and a bunch of filler missions inbetween that served no narrative purpose.