Assuming the scenario is "Twilight transforms into an Alicorn" (and it's not some dream sequence or temporary coronation spell, or some other hokey "GOTCHA" thing) then my gripe is their apparent disrespect for biology. Each of the races have distinct characteristics, histories, cultures etc and they're apparently going to twist her DNA around for the sake of a plot device (actually that sounds much cooler now that I write it out)
Though I'm not really sure what the deal with Cadence was, I'm assuming she was just born that way. Like, it's how they run their monarchy. Birthright, which I guess is how most surviving monarchies are. "Oh, you were born with wings AND a horn; you're the best of both worlds! You've got a bright future ahead of you!"
As far as the "episode" or "future of the show" is concerned I don't really mind either way - it can't be as bad as the Cadence/Shining Armour bumble, and that still turned out well enough. I just get the feeling they don't care that much about (or believe in) the world they've crafted if they're just going to twist it as they see fit
BUT THAT REMAINS TO BE SEEN