Maybe we're both reading too much into it, but the way they have Krystal as the premiere AT on the website, how she was given special attention on her reveal, and how even now she gets shown in trailers as a spirit does seem to at the very least indicate they're aware she's popular. I don't think this gives her any higher a chance to get in than some characters. For all we know, it's just Sakurai winking at how she's Fox's love interest.
I would love to see Krystal be playable, in a space suit like her Assault outfit, or maybe a new costume a la Wolf's. Bring back the Orbital Gate Assault level as her featured stage. Have her alt costumes be Fay, Miyu and Katt, perhaps. However, I don't think Sakurai cares all that much, sadly. I've learned to temper my expectations with Smash, as I'm disappointed 80% of the time.