Of the two options, I'd take EK.. as you will be on one ticket all the way through.
Note the EK Y legroom appears (I have never travelled this class, but observed it from J many times) to be a couple of inches more than most, but EK fit in an extra seat across and their seats are said to be a littel narrower - will this be a problem for you?
Entertainment is very good on EK and the stop at DXB will give you the chance to stretch your legs and look in the shops, if you wish to.
BTW, it is sometimes possible to get a free nightstop at DXB (even in economy), depending on the schedule timings. The hotel isn't the Ritz apparently, but peeps I know who stayed their say its survivable and breaks the journey.