Sorry, I disagree. I find the current situation perfect.
During the Nintendo Direct for XY, they have explicitly stated that they want the Pokémon Bank to continue in the future Generations, meaning it wouldn't be exclusively for Gen VI. So why include the Bank within Gen VI games?
I would also find it distasteful if the Gen VI games are constantly reminding me to pay for Bank subscription fee everytime I use Storage Box(in case I have the subscription cancelled). Moreover it's convenient for both Nintendo and Game Freak to update the Bank and tighten the app's security since Bank is an individual app; If the Bank and games are packed as one app, it's gonna pose more security issues, for example like game hackers.