I wouldn't say the "b" version is THE standard. its a standard, more specifically an IEEE standard (whcih is different from being the industry standard). But in the real world, there are pretty much no devices that use it. So in the real world, the "a" is the standard. Plus, I don't think the "b" version was even totally finalized until relatively recently.
As for why, I'm guessing it has something to do with the motherboards. I bet the 12 incher is using an older motherboard design or something like that. Something quick and dirty with a high profit margin (whcih is why it won't matter if it canibilizes iBook sales, it will have a higher profit margin, so apple would be happy if it did). So look for firewire 800 with coming updates.
On second thought, perhaps a more likely scenario is that they didn't want to redesign the 15 incher at all right now. It would look kind of dumb to have the 12 inch with firewire 800 and the 17 incher with it, but not the 15 incher. So probably when the 15 incher gets an update, you'll see it across the powerbook line. Either way it comes down to limiting how much money was spent on R&D for existing designs to accomodate a new technology.
It also gives the 17 incher, which probably has huge profit margins, a way to set itself apart, makign it easier to justify int he minds of people. This is good business. Offer something thats good, then offer something a bit better for a bit more money and watch the dollars roll in.
That said, I'm surprised they didn't make it standard. But I'm sure it will be soon enough.