Let's drop another log on this fire...
I can think of few characters Nintendo would've probably liked to have in SSBB than Snake.
Let's face it, Hideo Kojima has only been surpassed in his Nintendo-bashing by Chris Hecker said the Wii was two Gamecubes duct taped together, and Kojima's not too far behind him.
Between him calling the Gamecube a "Purple handbag" last gen and saying the Wii was "cable TV" compared to the PS3 which is a "theatre experience", then factor in the complete commercial failure of MGS:TS, I can't imagine Nintendo has much love for the bastard, if any.
Yet there's Snake, snapping the necks of beloved Nintendo characters across the board. My guess is that Sakurai had total creative freedom as one of the stipulations when it came to developing the game, hence why his little buddy Kojima could ask to put Snake in and it wouldn't be an issue.
Then, there's the fact that most of the MGS content in the game can't be found on Nintendo hardware, including the fact that Snake's isn't even the Snake from MGS:TS but from MGS2. It's like he went out of his way to put as much content not accessible on a Nintendo platform as possible.
Now, this is the part where speculation has to inevitably enter the equation. Do I KNOW that Miyamoto is miffed that Snake is breaking the necks of his characters in households all over the world (except Europe, but that's because I suspect Sakurai hates Europe for having so many languages)? No, but it's not exactly a stretch to assume he would be. Why wouldn't he be? Miyamoto has always shied away from the idea of M rated games and probably finds them horribly distasteful.
In his shoes, I wouldn't be happy, especially when the character doing this to MY characters was created by some asshole who can't find enough bad things to say about my company.
So yeah, speculation, but far from unreasonable.