I personally prefer Solid Snake over Big Boss. Kojima has admitted in the past that he prefers otherwise because he is, well, a clone. I kinda find that opinion rather contrived as I feel that Big Boss' story already had a predetermined ending but that Snake's story actually has room to grow. Because I mean, let's face it, as wacky as the MG saga gets with story, there's no way they couldn't write in a way to cure Snake of his genetic decomposition he was experiencing in MGS4 (nanomachines, son).
Beyond that, I have issues with Kojima's opinion about clones vs. humans. No offense, but even if they are a complete genetic copy, a clone is still human with feelings and everything else that comes with it. I think that a story about a man who is revealed to be a clone of a legendary soldier who has to unravel an international conspiracy to determine the future of humanity all the while having to live in the shadow of a non-existent father (whom he almost killed unknowingly) is far more compelling that the rise, fall and struggle of a soldier who, again, has a predetermined destiny.
Also, call me crazy but I think Kojima prefers Big Boss over Solid Snake because he's not proud of the quality of writing he brought to the table in the games that featured him. Don't get me wrong, I love the stories in these games but it seems that his statement coincides with his growth as a creator and no reasonable creator ever likes their early work.