I agree with the customizable bay idea but also that it probably won't happen. Whenever I hear rumors about moving the mechanical drive in the MBP to the SSD in the MBA, I wonder about how they're going to satisfy all of the people who don't care/know about read and write speeds but wonder why their storage space got cut in half.
I wonder if Apple pays any attention to the users who put a 2nd HD in the optical bay? Anecdotally, it seems common among power users, but I'd be curious to find out just how widespread it actually is. And you're right, even regular users will be baffled when their shiny new laptop has less storage than their crummy old one.
All I know is, unless affordable 2TB SSDs magically appear out of nowhere, I'm never going back.
If you look at the ipod, where the ipod classic has maxed out at 160gb and hasn't seen a refresh for 2.5 years you can see that they don't cater to the top 0.1% of users.
What they might have a problem with though is convincing the average user that their computers with 256 gb are actually better than the really cheap windows machine with 750gb, to a user that does seems like it's 3 times better.