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You don't like the current box system? Remember in BRY, this one was really annoying. As annoying as the bag system.
I think they have really improved it, and in BW it's just perfect.
It could probably be improved; being simple and intuitive is the best any user interface can be, while the current system isn't necessarily either and I can find it quite finicky at times. Game Freak seem to have left the third generation system as 'good enough' with only minor modification into future generations. Once the series moves beyond the DS, the box system could at least see a change of appearance.
I think it's a great system. There's nothing stopping anyone from alternating their team and if one could access any Pokémon at any time there would still be level gaps. As for the first box system... Let's just say that the newer boxes are a huge improvement on the original boxes and I'm glad for it.