The only advantage of Shinagawa is that it's easy to transfer from the Narita Express to the Shinkansen there. I've stayed there once, on a trip when I had to catch a 7:30AM Shinkansen the morning after my arrival. There's really nothing of interest outside the hotel (or inside the hotel, for that matter).

If you want to feel as if you're in Japan and not in Generic International Business Land, I like the more downscale Ueno or Asakusa areas. By downscale, I don't mean unsafe. But there's more of interest and more of real everyday life outside your hotel door (not to mention more affordable places to eat and shop) in Ueno or Asakusa than in Shinagawa or the Tokyo Station area.