Hi,
I have stayed at the Miyako a two times in the past two months. Although it's true that the decor is a little worse for the wear, I like it there, mainly because of its central location (although I should clarify that I'm not interested in close access to most of the tourist attractions). I definitely recommend the Tower Corner rooms. I've stayed in a standard King and a Tower Corner King, and there's no comparison. The standard room I had shared a balcony with another room, which is a little creepy if you're a woman traveling alone. The Tower Corner rooms are about twice as large and have two private balconies with two different views. Also, the bath/shower area in the Tower Corner rooms is much nicer. The shower/bath in the standard rooms is kind of closed in and dark, but the Tower Corners have glass separating the shower/bath from the vanity area, so there's much more light. Definitely try to stay in a Tower Corner room if you go.

I also consider it one of the best places to stay in the city if you have a rental car. Most of the Union Square hotels charge $35-$50 for in/out parking. At the Miyako, parking for guests is free during the day (although, be warned, it's a very small lot, and it's first come, first served). If you keep your car in the hotel lot overnight, it's $22, but you can easily move it to the Japantown lot overnight (two blocks away), which I believe is $13. But I'm notoriously cheap, so I usually keep it in the hotel lot during the day and then move it to the street at night after the meters are no longer monitored, then move it back to the hotel lot in the morning.

Hope that helps... If you have more specific questions, just post them, and I'll try to respond.