You obviously don't have a very strong grasp on how working with code works, because you keep spouting this as if it will be an issue, when it pretty obviously isn't.
I know enough to know that cross gen compatibility is not simple enough for a one size fits all program to communicate with each and every one, that's absolutely ridiculous. It would have to be constantly updated with each new Pokemon generation, and then when a new handheld is released it has to be designed to work on those consoles. The idea that you can simply let it sit there forever without having to actually do anything is utterly laughable.
The program may need to be rewritten and reprogrammed, but like any program that stores data, the Bank will probably write all the information to a secure database which is inherently separate from the program itself. So let's say the hypothetical next-generation handheld nintendo console comes out, all they need to write is a set of a code to handle accessing said database and transferring your Pokemon from database to whatever media the game itself is stored on. It's an ideal solution because the technology storing the information about your Pokemon is totally separated from the technology that's used to access and transfer said Pokemon. Incidentally, PokeBank also means that they can write games for other system - for instance, a Colosseum-type game from the WiiU - and as long as they have the appropriate code, they can allow that game to transfer and deposit Pokemon at will.
No matter how you feel about the maintenance fee, this is actually the best possible solution for both transferring and storing of Pokemon in the long term. Cloud storage is something that is relatively easy to access and, thanks to how it works, is a real long-term solution for the issue of cross-generational transfer. Everything else that Gamefreak and Nintendo have done have essentially been stopgap measures that leave us in the same situation we were in before yesterday: not knowing whether it would actually be possible to transfer Pokemon.
If you want to doubt Gamefreak or if you simply don't want to pay, then that's your right, but considering the options and the available technology, this is the best solution and I applaud them for implementing it. I'll gladly shell out five dollars a year for this service.