Great experience
We loved this hotel. We booked directly through their website instead of using hotel.com or other go-between companies (don't know if that might be why people have problems here). We booked a smoking room (only cause it was cheaper) double in the Annex tower for 7 nights. We didn't pay at that time of reservation, so all we had was a printout of an e-mail confirmation. I was afraid that since we weren't allowed to pay in advance or pay a deposit that we would have problems. But on the contrary, check-in was very smooth. They asked us if we wanted a non-smoking room instead, and we said yes, thinking we'd see an increase in price, but it didn't (paid a little over $100 per night, which I don't think is bad for a great location in the middle of one of the biggest cities in the world). We were on the 17th floor and had a good view and huge king size bed. Room was a decent size and the bathroom was very nice and big good size. Room had a desk/chair, a vanity/stool, another small table, 3 drawers and a closet. Of course, if you're accustomed to grand hotel rooms, this would clearly not be the choice for you. It was simple, very clean, and had a great flat screen TV.
A long distance call from the room cost us ~$1.75 for a minute or two. Was happy with that. Also, we found out that we had free internet in our room... apparently they charge the other towers, but not the annex tower. Sweet!
We were also able to save money by only having our room cleaned every other day. I heard about this before we arrived, but did not know about the paperwork involved. There is a green form included in the papers that are in the room upon your arrival. It's part of some kind of 'go green'/'save the environment' program. You just put your name and room number on the form and leave it on your bed. They'll get your trash, but not clean or make the bed. Go to the desk later and they'll give you a $5 coupon for every person staying in your room. By the end of a week-long stay, a couple can accumulate about $30 worth of free entertainment/food, which really helps on a tight budget!
As many have said, the location can't be beat, especially for first-timers to Tokyo. It's right across the road from the train/subway station. When we got on the Yamanote line/inner circle, it was less than 20 minutes either way on the loop to nearly everything we had on our list. There is a bullet train that goes straight to Kyoto from the Shinagawa station and also, the Limited Express from Narita goes straight to Shinagawa also.
The only downfall was that the bed and pillow were on the hard side, but it did its job... We were so killed when we came in at night that I would have slept on the floor.
Overall, loved it and would definitely stay again.