Game Freak uses Pokemon Bank for transferring because of connectivity restrictions. The 3DS games aren't able to connect to DS games (Download play can't go 3DS to DS). It's not like Gen IV, where D/P could connect to the GBA games via the dual slot feature of the DS Phat/Lite.
Honestly, $5 for a yearly subscription to Bank isn't bad at all. Hell, I still have $5 of leftover credit on my eShop balance from Smash Bros DLC. Game Freak could've just left us high and dry in terms of transferring previous gen Pokemon and made us start from scratch, akin to the Ruby/Sapphire days.