For several years, I am using Air France-KLM when I was going back to Japan. Then, due to KLM does not fly to Tokyo Haneda airport, I mostly use Air France flights from/to Paris CDG to Tokyo Haneda.
Although it is not the cheapest flight between Europe and Japan, I prefer Air France due to
1) It is one of the 5 airlines flying between Europe and Haneda airport.
2) Air France has evening flight from CDG to Haneda and Haneda to CDG.
3) There are several flights per day.
Evening flight is quite important. For example, if you fly in the evening from Haneda, you have almost full day on the day of the departure. You can pack your back on the last day and do not have to wake up so early. Flight from Paris is also late therefore you can work on the day before flying to Japan.
Also the airport difference in Tokyo is important factor. Narita airport is 70 km away from downtown Tokyo and transportation will cost much more than Haneda airport. In case I use airport bus from Narita to my hometown, it will be double than Haneda - hometown fare. Also the buses run much more frequently between my hometown, Tokorozawa than Nairta - Tokokorozawa.
Then, Air France and KLM is a single company, you can also choose KLM flight in case Air France flight does not suit you.