Sponichi posted an article listing a few roadblocks that would have to be cleared if any sort of Global World Series is to be played.
Finances - how will the event be funded
Player contracts - the MLB would likely have to delay free agency if the GWS were to take place after the World Series
Venue - where to play the games
Timing - when to play the games
Baseballs - similar to the problems with the WBC, the two leagues use different kinds of balls (this is likely more a problem that Japan needs to deal with)