JAL has redesigned its domestic flights seat selection site. Now the seat map will be more closely resemble the actual configuration. They will even mark seats with extra legroom (well they called it extra foot room). Also more seats will be released for selection at 5pm the day before your departure date. More details here:
http://www.jal.co.jp/en/dom/service/jizen/
I hope marking seats with extra legroom isn't their first step of trying to sell those seats to non-elites