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.jp and .co.jp domains are both still quite expensive to obtain. A .com or .net is only a fraction of the cost. I still see a lot of advertisements for sites that don't use Japanese local domains at all. That's a telling sign especially when a lot of them specifically instruct users to search for specific keywords on the advertisements themselves.
I can certainly see the logic in ranking a .co.jp over a .jp in terms of quality. The application process is quite a bit more difficult and restrictive. However, I've also seen cases like the recent opening of Baidu Japan where their baidu.co.jp is still owned by another company that appears to have obtained the name for other purposes.
Does anyone have some data on this they would be willing to share?
I had a few conversations with Japanese people about domains over the Obon holidays and was surprised that many of them thought that a .co.jp was much more prestigious. These people were not internet savvy at all. These were business owners who wanted websites. When I explained the additional costs and procedures that were necessary for a .co.jp name that only enamored them more.
What could I take away from this? Not much. ;) But I might think that the informed consumer could and probably does realize the value of a .co.jp over a plain .jp name. This has nothing to do with the SEs, obviously. It's something to take into consideration though.