Obviously, Team Flare has infiltrated into Gamefreak and are using the annual fee to make more money. After all, money is what they're after.
I can see it clearly now. Pokémon Bank, how clever!!!
Because it doesn't take money to run a server. But sure, let's make it free, not have enough to maintain it, then have all our Pokemon deleted from the system because of it.
I was just joking about Team Flare. :P
I actually love the concept of Pokémon Bank and the annual fee. xD
@The Outrage; someone on smogon calculated that if the pokémon datastructure remains the same it takes about 400kb to store 3000 pokemon. 400kb storage on a normal cloud server service would cost less than a cent a year. The money they earn from pokémon bank is pure profit for game freak at these prices.