It's not necessarily that Kanto is favoured when it comes to the Dexit policy of these games, but the way Kanto 'mons are consistently given the new tools of each generation in a way other gens aren't, it still creates the impression that Kanto 'mons will be favoured going forward. Maybe not in terms of inclusion in this game, or the next, or possibly ever, but the impression stands that the other generations aren't cared about to the same degree. There will always be hope for obscure Kanto 'mons to be brought to the limelight through the gimmick du jour, while obscure Sinnoh or Kalos 'mons appear doomed to stay obscure forever. Gotta have that sixth alternate form of Lickitung before Carnivine can get something.
And it's this impression of favouritism that shapes the views of long-term fans. Maybe the favourite Pokémon won't be axed from the games forever, but that impression that the chance is half'n'half at best can quickly kill the enthusiasm for the games. For now, it might be two separate truths that 1) TPC favours Kanto, and 2) not all Pokémon will be in the games going forward, but fans are going to see them in light of each other, mix them up, and decide that there's writing on the wall and it's not boding well for their prospects of future enjoyment of the franchise.
What I'm saying is, the franchise doesn't have to actually be devolving into a complete Kanto pander-fest where all other generations are neglected, but the impression that it is can still take root in fan circles. And if that idea settles and spreads into the wider Internet culture, the whole image of Pokémon may go belly-up.