I always look at both sides of the coin before hopping on a bandwagon if I'm interested. This doesn't sound like a bad idea in hindsight, but there are many things to consider that make me rather just stick with the traditional way of trading Pokemon.
I didn't see any indication you couldn't still do traditional trades using Wi-Fi/ADHOC connections. The Bank seems completely separate.
-The eventual termination or cleansing of the servers. It's going to happen eventually. Maybe there will be enough time for people to migrate their things over to the next generation servers or what not. Who knows at this point in time? All I know is, if it's too good to be true, then it more than likely is.
Pokemon games usually retain their popularity throughout the entire lifespan of a handheld and beyond. I would say it's highly unlikely that Nintendo would want the bad press associated with shutting down one of their biggest games' servers prematurely. Will it be shut down in 5 years? Possibly, but that's 5 years and up to 5 new games later. Plus, this sure seems more like its laying the groundwork for a universal system that could be used to transfer Pokemon between future games as well. If that's the case, this is utterly brilliant and will have a lot of mass appeal. You can send things from game to game without having to have 2 systems to trade to yourself.
-Potential rise in the annual fee. Right now, to most people, it's throwaway money, but it's not the case for everyone, especially kids who have strict parents. In addition, not everyone is willing to spend money on something trivial for a game, similar to DLC or Microtransactions. There is to be a free trial, but then that's it.
Isn't it $5 a year? No matter how strict one's parents are, that could be saved up by collecting change throughout a year. Again, I don't think Nintendo would want the bad press associated with raising it, either.
-Server Hacks. Sure, it's Nintendo, they're going to have security. But Sony, though. If Sony, then Nintendo has the same possibility of happening too.
This is always a risk, but your main data would still be on your system, so a majority of what you're doing wouldn't be affected.
-Connection Issues. Not everyone has perfect internet or Fios. So we've got lag issues and disconnection issues commonplace with cheap internet users. What happens if that defects the upload process to the server? Are they just going tp lose the Pokemon that didn't transfer completely? Are they going to unintentionally upload a Missing No? Who knows.
Unlikely. If it's anything like most databases, it will image your current box before making changes. Then, when you finalize the changes, it sends the signal to the server. Nothing is saved until this point. So, if there's a connection interruption, the box would revert to it's previous state. Worst case scenario stuff does get damaged, you could probably contact Nintendo and request them to restore the box to a previous state. I'm going based on how MMOs often work and how other online databases work here, but I'd be shocked if this isn't how the service would operate.
I could go on, but these are the major, eye catching things I foresee at the moment.