Business sense tells you the almighty dollar with prevail and as long as you keep making money you will keep doing something.
I want to bring up an interesting point though, with Mario and Zelda and the other long running game series out there, you don't have to have the previous games or system to enjoy the game on the current console. Does it help with the story, easter eggs and for more enjoyment? Of course it does. But you didn't have to play Link's Awakening in order to complete and finish Ocarina of Time.
That is where they are going to run into their big problem, is this completing of the pokedex, obtaining the Pokemon, it will be or become unwieldy and impractical to be able to capture all 700+ Pokemon. You have to have had Pokemon Ruby/Sapphire/Emerald to complete Diamond/Pearl/Platinum, which you would need to complete Black/White/BW2. I think there comes a point in time where you allow 99% of the Pokemon to be caught between two versions and you won't worry about having to transfer or find someone to trade with etc.
I think as time goes on we will see DLC where they implement the ability to catch new pokemon by giving us new pieces of the region or perhaps pieces of old regions.
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