This discussion has been played out in the Luxury Hotels forum already, by the way, so the OP may want to look there.
Not sure what's not to like about the Pen, especially on a 2-4-1 suite deal. The public areas are a bit small, and it needs a decent hotel shop, but the location is fantastic for most things, you are in a stand-alone building rather than in an office tower and the suite I had - which came in at 50,000 yen per day I think, the same price as a standard room on 2-4-1 - was beautiful.