Fair enough. But I think that's kind of a false equivalency. First of all, Smash 64 was a very different beast. There were no expectations placed on that game, and so Sakurai could pick who he wanted without having to worry too much about "hype". I have a feeling that if Earthbound had not been represented then, Ness would probably be considered more of a Saki or Andy in terms of his chances now. A cult character from a beloved but underplayed and under-recognized game. You're right that Ness being designated as one of the "faces of Nintendo" has a lot to do with why the Mother series has received so much attention since then. Shulk is a cult character too, but for some reason people consider him a shoe in.
In addition, the protagonist of the best RPG "on the Wii" is not equivalent to the protagonist of one of the most unique and influential RPG's of all time, created by a Japanese cultural icon. Plus Ness does a lot more to distinguish himself from any number of generic JRPG protagonists than Shulk does. My issue, I guess, is less with Shulk's obscurity and more with his uniqueness. The main thing counting against him is the fact that he's a "handsome white guy with messy blond hair who wears a little vest with too many zippers, and has a giant magical sword that he somehow wields one-handed". I'm sure he has a unique personality, but to anyone who hasn't played Xenoblade, he just looks like Cloud, Sora, Squall, Tidus, Zidane, etc.
If Sakurai feels that "JRPG dude" is an archetype that Smash is worse off for lacking, then Shulk is a fine choice to fill that hole. I just don't think he would pick this character when there are so many others who are much more uniquely "Nintendo", you know what I mean? He just doesn't feel like a "Nintendo" character, and to me at least, would feel really out of place next to Mario and Kirby. Sure, Snake and all that, yada yada. But like Ness, Snake is the protagonist of one of the most unique and influential series of all time. Shulk does not have that going for him.