A new storyline (as opposed to one occurring around the same time as the games in existence) spanning multiple regions would be really, really cool, and I'd love to get it, but I can't see them doing it for what's already been stated. Technical limitations, necessity of console, and it would be quite a hassle to complete a storyline that involved such a chase with multiple teams; even then, they'd have to find out various ways to ensure you don't get to keep your Pokemon on every region, so you have to start from the beginning again instead of having a level 62 Charizard burning Johto to the ground.
This IS possible on a console if you think about it, as long as it has an original plot and your Pokemon get stolen from you on your way to Hoenn, and you get a new starter in Slateport to make up for it. You then take on Hoenn and try to get your Pokemon back from the International Syndicate that stole them.
I honestly don't expect them to do it at all, and if they did, they wouldn't do it right. Has GameFreak EVER developed a game for a console? Hasn't Nintendo licensed the games to other companies? The Stadium games were developed by HAL Labs, which also does SSB, and Colosseum and XD weren't GameFreak...
I really don't know what to expect from something like that, but it'd need to be an original story intertwining several characters from all the games. It could be done, it'd just be a huge-budget game that would be make-or-break for possibly all of Nintendo.