They'll definitely cut Jynx. It was one of the few from its set of 'mons that didn't get any focus in the later gens because of its racial implications (it even got a color change to purple from black). Gen 2 was the last connection to Jynx (Smoochum).
Almost all the late numbered gen 1 'mons got something down the line except 3 (Lapras, Tauros, and Ditto):
Eevee got Sylveon in Gen 6
Scyther got Mega Scizor in Gen 6
Pinser got Mega Pinser in Gen 6
Kangaskhan got Mega Kangaskhan in Gen 6
Rhyhorn got Rhyperior in Gen 4
Electabuzz got Electivire in Gen 4
Magmar got Magmortar in Gen 4
Snorlax got Munchlax in Gen 4
Mr. Mime got Mime Jr. in Gen 4
Pretty much everything around Jynx in the Pokedex got something.
As a proud fan of Jynx, I have to say "the connection" you talk about might be missing from Jynx, but that's not the point.
She was still included in the Kalos Pokédex, just like Mr. Mime, so both of them have the same chances (of getting cut). Or being in, since there aren't many Ice or Fairy Types. Jynx was even featured in a Pokémon Go event not too long ago, so it's not like they're trying to ignore her.
The other Pokémon I've seen mentioned is Porygon, but it even appears as a Pokédex in the Pokémon Masters artwork.
The thing is for more that I think about it, no reason is strong enough for me to say, this or that Pokémon would be ok if they're cut, or would actually make sense that they're cut. I could probably think of Pansage, Pansear and Panpour, and that's it lol but I really don't know how they think.
Most of the Pokémon had been some sort of featured here and there in recent years, whether is the anime, spin off's, TCG, and all of that must be taken into consideration, because with these new games, there's all the merchandise and the anime that come along with it.