My son worked there when he was in college, so we always stayed there when in SF. It's authentically Japanese and most of the odd little touches you see have a purpose. They are very serious about meeting the expectations of the Japanese guests.
They have tatami rooms, in which the mattress is traditionally on the floor. These rooms have valuable silk comforters, which unfortunately were stuffed into an odd white cover to keep them from shredding on the tatami mats. They also have regular western rooms. The higher-up corner rooms, which are larger, have great views. The windows are covered with Japanese screens, and shoji screens which were constructed by a craftsman brought in from Japan. Each room has a meditation spot with a statue of some sort. The soaking tubs are deep but not attractive, specially constructed for the Japanese customers, and the bathing areas are tiled with a low faucet and stool for a pre-soak washup.
I haven't stayed there in a few years as we no longer get the special employee rate, but it seems to me the rooms could have used a remake several years a ago.
I think room service uses Denny's across the street in the Best Western Miyako.
Location is good, although it's on the edge of the Western Addition and gets slightly dicey towards Divisidero.