I think the lot of you are putting too much stock into the whole kept you waiting thing, do you really believe Sakurai would go to Nintendo and tell them hey lets keep Snake a secret character just so we can make an obscure reference that only metal gear fans will understand.
To someone who hasn't played MGS, it seems dumb. But to those who have played MGS, it's as big as the "Snake? Snake? SNAAAAKE!" line, if not bigger, since it has been in every MGS game, including Revengeance, and was even in the Subspace (the line was also the only thing actually spoken in the subspace). It is a reference that only fans would get, but then again, most of the people who care about Snake returning are MGS fans, and would get the reference. The only other people who want him to return are people who don't want to waste a good moveset, but thats a very small group (compared to the MGS fans).
At the end of the day, Nintendo doesn't care if Snake is in, so they don't care how Snake is revealed. From Sakurai and Kojima's POV, it's a funny way to reveal a character, though from our POV, it has required us to wait a long
time. I know it sounds crazy right now, and it might be, and we just haven't realized it yet, because we're blinded by how much we want him, but if there is any third party who is going to be revealed this late, it's Snake.