I think the primary reason why they are complaining is because of the fact it promotes stereotypes that make it more difficult for foreigners who intend on being permanent residents there to be accepted. In japan foreigners are seen as either casual or temp. visitors as a result they are not seen as being able to speak japanese fluently, can't eat chop sticks, etc. Anyone actually intends to stay longer or stay permanently is seen as weird and as a result hostility, although not necessarily violent, begins to escalate against them and they start to become shut out from the society. You will notice that the groups mentioned in the article that are complaining are those that represent foreigners in japan who intend on staying there permantely or for several years like a decade.
This is what one of the commenters said on debito blog
"Having read all of the commentaries here and everywhere I can see that most of the people just don?t get the real issue with macj ?Mr. James?. The problem is not about racism, he could have been african american too, the problem is that it promotes a stereotype of foreigners in Japan, they can only speak in katakana, they are goofy enough to be treated by their first names and they are crazy about the ?cool? things they discover in Japan (as with the NHK program).
As long as this stereotype remains the foreign residents are not going to be treated fairly and with equal consideration other than being casual or temporary visitors in here."
Here is another comment:
"One interesting note about the ?Mr. James? ads: There aren?t any in the McDonalds across from Kamiyacho Station, just down the hill from the Hotel Okura. This is a gaijin-heavy area, with lots of us staying in the hotel or working in the offices nearby. If the ?Mr. James? ads are so inoffensive, why is McDonalds Japan keeping them out of its restaurants in foreigner-heavy neighborhoods?"