Lords of Shadow by far, in my opinion. I prefer the stage-by stage setup, ACTUAL PRESENCE OF PLATFORMING, art direction, atmosphere(not the same thing as art direction) and combat setup.
CoD does have a badassly revamped Trevor Belmont, a killer soundtrack, an AMAZING Dracula battle at the end, and continuity with the past storyline.
I just like LoS better. As a Castlevania game, and as a general game. These two are vastly different games though. As others have pointed out, LoS vs. LoI would have made more sense, since the have a lot more in common.