I wouldn't say it "bombed" at all. According to VGChartz, the title sold a little over 720,000 copies, and that's not even including digital sales. In my opinion, a port of a game that had very little changed when it was ported over selling 700,000+ copies overall isn't bad sales at all.
EDIT: http://www.ign.com/a...g-sales-figures
According to this, about 20% of Star Fox 64 3D's sales were made digitally as of April 17th, 2013. So 720,000 copies times 20% = 144,000 copies.
So a nearly straight-up port of a game sold at least 860,000 copies. Now, there must've been very little investment put into SF643D. Just to compare, I'm sure Fire Emblem: Awakening had waaaay more money dropped into it, sold around the same amount of copies as Star Fox 64 3D, and Nintendo was very, very pleased with the sales of the game.
So yeah. StarFox is nowhere near dead.