It tickles me with delight, this whole notion of major game characters vs. major game characters. Although there are those who would say Brawl should remain a Nintendo character driven fighter, I find the 3rd party characters the only real earth shattering addition Nintendo's making to Smash Bros. The question of whether or not Nintendo should is basically moot at this point, they already crossed the line. Now it's a question of how many, and which ones.
I must say however, there isn't another company out there that could be as good of a host as Nintendo to an all-star "Brawl", and no other fighter could be as receptive to throwing a mish-mash of completely different characters into the same arena together. With Smash's not-so-serious combat and playful attitude, there's never any one character that appears overly menacing towards another (Although Bowser does seem to have a sweet tooth for JigglyPuff), and Smash really strikes a fine balance between "This character is cool", and "This character totally ROCKS!".
That said, Sam Fisher(SplinterCell) makes perfect sense as a Ubisoft character, and was most likely included as one of the four potential "representitive" characters Ubisoft sent Nintendo's way. After all, if Solid Snake can make it into Smash Brothers, then dang it we'd better see Sam Fisher in the next crate on its way into Brawl!