I think that, for the people who really take their website serious, and are honest with themselves about their level of expertise with design (or lack thereof), they'll continue using themes and easier to set up options.

Some people get overwhelmed at the amount of editable areas there are in some themes options panels, so I doubt they're going to feel comfortable designing everything themselves.

And then on the other side of the token, there's the crowd who want to stylize everything themselves and blogs will start looking like Myspace pages, circa 2005.

The cream will always rise to the top.