I have maintained since 2010 that if Generations 1 & 5 were switched, we'd get the same complaints we do but about the Gen 1 Pokémon.
I know I'm biased here, but I honestly don't think Pokemon would have seen the same level of popularity with that set of designs. Pokemon was an international cultural phenomenon for a reason, and I really don't see it having taken off in the same way if it had launched so drastically different.
Even just comparing the designs from each of those regions (and while trying to be as objective as possible), I think the Kanto designs are more broadly appealing. I mean, the Gen V starters have their fans of course, but the Kanto trio were admittedly pretty 'safe' designs in that a fire breathing dragon, a dinosaur and a massive Turtle with cannons on its back would all be really 'cool' to kids. Compare that to the green Snake, fire-Pig and whatever the hell you'd describe Samurott as, and I just don't see them being as popular.
What is the mascot in this alternate reality? Emolga? Does Unova have a legendary that would be as popular as Mewtwo? I know Genesect pretty much ripped off Mewtwo's origin, but I really think the design of Mewtwo (and Mew) were key to their popularity.
I asked the question here a few weeks ago "what are the most popular Gen V Pokemon", and pretty much everyone had a different answer. It seems the popularity of the Pokemon is a lot more spread out when it comes to Unova designs, and I think that would have really limited its appeal back then. Compare that to the massive popularity of Pikachu, the Kanto starters, Mewtwo & Mew, Eevee, Gyarados, Gengar, Arcanine, Machamp, Dragonite, Nidoking...it was really a handful of designs that propelled Pokemon to such heights back in the day imo, and I don't think Unova has many designs with mass-appeal like that.