patrick.net

MarkInSF says

Actually, saying the increase in median price from 1940-2000 is fully accounted for by changes in size and other improvements is a different assertion than saying a home that was standing in 1940, that is still as is today has tracked inflation.

It pretty much is the same thing.
The WSJ article you cited says

Mr. Shiller's chart shows that home prices from 1940 through 2000 rose at an annual real, or inflation-adjusted, rate of 0.7%. Data from the Census Bureau, however, puts the real rate at 2.3% for that period. Part of the difference may be due to improvements in the quality of homes, Mr. Lawler says, but he doubts that accounts for the whole gap.

Mr. Shiller responds in an email that much of the difference "is indeed caused by quality change." He cites Census data showing that nearly a third of American homes lacked running water in 1940.

Both Lawler and Shiller agree that is what it means.

MarkInSF says

It is entirely possible that appreciation is very slow initially after new construction, not even keeping up with inflation, but accelerates as the house gets older, and it’s land value become a greater component of it’s value due to crowding.

I agree. A new house structure should depreciate at first, and that depreciation could offset or outpace appreciation of land. The index does not apply perfectly for any particular home be it new, old, in a tony neighborhood or in Detroit, so expecting that kind of accuracy is asking too much. The current methodology only reflects the average growth in a particular market. They define the average as the aggregate price. So each percent appreciation is weighted by the house price.

MarkInSF says

Another data check: http://www.census.gov/const/pricerega.pdf shows the inflation adjusted median home price going up 24% from 1963-1975. BLS/Shiller sho

Those look like new construction prices. The median price of all sales in 2000 was $120,000. That link shows $169,000, which is the median price for new construction. As you said, most new construction is in the region where a city is expanding and land values are increasing the most.

ch_tah says

If you are trying to support the notion that Shiller is great at predictions, I wouldn’t link an article that shows he was early by 5 years in calling the peak, not to mention the fact that for some parts of the BA, he’s still just flat out wrong and prices are well above their 2002 prices.

I think the bubble would have popped MUCH earlier had the government not heavily intervened in the market. By all rights it shouldn't have taken 5 years. He simply called it as being a bubble, and he was right.