I'm not going to touch the whole Sci-Fi vs Fantasy genre thing, as both do actually have some ties and other technicalities involved iirc.
That aside, I think PsychoJosh makes some very good points. I already made a somewhat similar point about being open to the possibility of Krystal not using the staff due to it being dropped from the series.
Within Star Fox itself, it makes little sense for her to have it given Star Fox's setting and gameplay focus which is more than likely why it didn't appear again in Assault or Command. (And of course the fact that Adventures was changed into a Star Fox title at the last minute, hence why a lot of it doesn't mesh as well with the rest of the series.)
Within Smash Bros. however, it's no longer an issue as it's a non-canon crossover so a staff wielding Krystal in this case would fit in just fine.
The main issue however is that many fans want her to have the staff either due to a fondness for Adventures or out of fear that she'll be a clone without it (or both.) The problem with this, is something that I'd compare to Jr. supporters wanting him with his paintbrush. Krystal, like Jr. moved on from using their original weapon, and it's not actually integral to their character.
So if Krystal returns in the next game, and is once again without her staff, and they continue to focus on new weapons and equipment, I think it stands to reason that rather than mold Star Fox to include things that were haphazardly added to it, they'll instead mold Krystal to fit into Star Fox better.
If her future appearances continue to not use her original staff, (which they likely won't) and she's provided with new tools, then why would they go all the way back to Adventures to represent the character in Smash if that has long since not been part of the character's focus.
That said, if possible, I would like them to reintroduce her with a staff like weapon more fitting to the series. One based on technology as opposed to magic with stuff like a built blaster and whatnot. It'd give her a staff as a nod to Adventures and fulfill the desire of those that want her to keep the staff while adapting it to better fit the series.
Though the biggest issue facing Krystal right now is whether or not she'll be making a return now that the series has been rebooted. iirc, I believe they said they're still interested in having her return in the future, so let's hope they deliver on it and actually do it well this time.