At the risk of jumping in way too late to be useful....

I'm a big fan of the Hyatt Regency. Way cheaper than the Park Hyatt (which you can see on the other end of Shinjuku Central Park) for essentially the same location. I happen to like the location--close, but not too close to everything with a few places right at hand. But, and this is big to me, the club floor rooms are much nicer than the standard rooms. Depending on the rates you get, it may or not be worth it to you, but compared to the standard room I stayed in, the club floor rooms have been much more recently updated and are that much more pleasant. (Nota bene: I've never stayed at the Park Hyatt, but I'd sure like to )

The breakfast in the lounge is plenty for me--croissants and other bread items, eggs of some type (scrambled/quiche), bacon, sausages, and salad plus various beverages--to be of value. The evening service has changed in the last year to be a sit down service (choice of 2 items) in addition to standard cheese, crackers, nuts, beer, wine, alcohol. And it was no where near as crowded last week as in years past .