>>32871078I feel that all depends on how Nintendo is going to handle putting the Switch forward as their primary handheld console, and therefore how the Pokemon Company and GameFreak want to handle the next generation of games.
The very best, dream option would be that they port all of the games to the switch as Virtual Console titles, and upgrade the Bank to allow Pokemon to migrate up generations quickly and easily.
I honestly don't think they have any excuse to nuke Transporter; it comes with the Bank, and if the next generation of games will be on the Switch, they'll migrate the Bank to the Switch as well. So theoretically, as long as your 3DS works and your Bank account is active, you should be able to migrate up for several years.