My understanding is that the Nexus 4 (out of stock in the US) is the 'pure' Android phone that Google designed, Also, Nexus should now be 4.2.1 vs. an earlier version of Jelly Bean.
The Samsung phones have more of a Samsung skin, so they may behave a little differently in the details.
Will the Nexus 4 ever get back in stock in the US? Or will it be the Nexus 5? I wonder.