For what it's worth, Robin was in as recent of a game as his competition (Chrom), meaning relevancy wasn't a problem and he was able to get the nod based on his vastly higher moveset potential.
Greninja's more worth looking at, though. X and Y were over a year away when he was decided on, meaning Sakurai picked him solely on moveset potential and distinctness from the rest of the roster. He was able to fall back on the fact that Greninja's games came out almost a year before SSB4 is getting released, meaning that unless something disastrous happened Greninja would be relevant then...and he was.
What we don't know is how long they've been talking about this new Star Fox game, or if there'd been a WIP release window for it two years ago. We know they've been tossing ideas around for years, but if they'd been discussing it more seriously back in 2012 and got sidetracked somehow, Sakurai could've thought Krystal would become relevant enough again to where her high moveset potential would make her worth adding to the roster.
It's a bit of a reach, admittedly. >_>