Well, my normal position on a lot of theories like this (Cubone is an orphan Kangaskhan, Gengar is Clefairy’s shadow, you killed your rival’s Raticate, etc) is that I think they’re a lot of fun and, if they’re consistent with the evidence, I would probably roll with them if I were writing a fan fic or something just because they add extra details to the world, but I just don’t think there’s enough there to demonstrate that the creators intended for us to make those connections. I guess then you get into Death of the Author stuff, but that still makes my head spin, so let’s not go there.
Anyway this theory.
I was going to say that Genesect was a jungle Pokémon originally, but I can’t remember where I read that now, so I suppose I may have just made it up… still, I am bothered that Genesect has no water-related abilities at all (aside from the Water Techno Blast), since Kabutops is primarily an aquatic Pokémon. The Pokédex does suggest that Kabutops was a transitional state in the adaptation of a species of Pokémon to life on land, though, so I’d be happier suggesting that Genesect was a descendant of Kabutops who’d more fully committed to a terrestrial lifestyle (I don’t think Kabutops’ age ever has been specified, actually; he could well be older than Genesect).
As for Genesect being a Unova Pokémon and Kabutops a Kanto Pokémon… well, do remember we’ve got 300 million years of continental drift (or… Kyogre/Groudon antics… or Regigigas towing landmasses around… or whatever) to account for. Kanto and Unova could well have been neighboring regions once. The workers at Twist Mountain find remains of all the known fossil Pokémon, so I have to assume Kabutops did in fact exist in Unova at some point.
Pokémaniacal 