The most glaring difference is that of the clear religious overtones (not undertones). From different songs sung to other obvious symbols, it is a little contrary to the non-religious, agnostic may be a more appropriate term here, stance that is held regarding the consideration of members, although a belief in G-d is required to join. It leaves someone like myself, who is not Christian but who is very familiar with Christianity, a little confused as to the true direction.
However, like many things in this country that have significant Christian overtones, one needs to consider the spirit of the message rather than the references made. Additionally, when looking at many of the other aspects of the ritual and the general set up and structure of the meeting there are numerous Jewish references, symbols, and undercurrents in the order. Most glaringly is the fact that we face the East toward the temple mount and Jerusalem (this is a commonality found throughout Freemasonry).