Which one I prefer very much depends on where I'm coming from and going to!
Thameslink has marginally more preferable trains, to me - although that's tempered by the fact I've very rarely got to use the EL for outer suburban journeys while I regularly use Thameslink from St Pancras or Farringdon to beyond Haywards Heath. However the station environment and passenger experience of the infrastructure on EL is much much better, as you'd expect from a brand new line. Although I've only used the EL 1 time.