Last time this was thread was open I discussed Pokemon that may come into conflict with the time period and as such may be omitted from the dex, namely Rotom and the Porygon family. Since then I've thought of some more Pokemon who may fall into this criteria.
The fossils may very well be goners. I was initially thinking they could justify them still being in the wild but then I looked deeper into the lore and realized these dudes' heyday dates back to hundreds of millions of years ago. I guess they could tuck in a hideaway in Mt. Coronet somewhere, but otherwise with technology to revive fossils not being around yet it's bye bye for these guys.
Wait a minute, you might be thinking, wasn't Magmortar in the footage? And yeah, it was. The problem with these Pokemon isn't with themselves, but their evo items.
The Electrizer and Magmarizer both look very artificial, like items that couldn't possibly exist at this time unlike the Protector or even the Metal Coat. Maybe they'll come up with alternate evolution methods, maybe they just won't acknowledge the discrepancy, who knows.