I thought both the "old" STBII (w/o the channel 3/4 switch) and the "new" one (with the switch) came with the newer remote. The original iView (STB, w/o the II) came with a different remote (although STB owners can buy the new remote separately and load a firmware update for it).
But IIRC the "new" STBII powers down the USB port in standby. The original STB did this too, but the "old" STBII did not. That would be an advantage for the new STBIIs, if you don't like running a USB-attached HDD 24/7: it would reduce heat produced by the iView's power supply, hopefully extending its life.