Main generation Pokémon games almost always come with two versions. What do you think of this? Would you prefer a single version, or do you like it being two?
I don't think that the two versions should continue, no. It's outdated. Even if their original idea was to encourage trading, I think a different way to achieve that would be coding different copies (or perhaps just randomizing when a new save is made) of one game with a couple or few different variations of Pokemon to be found.
I don't know how technically complicated that would be to achieve. I'm not a programmer. I suspect that the only reason they make two versions is for the money, so I don't see this ever changing even if my solution were to be feasible.