Like most people seem to be saying, I prefer 999 for its generally better, tighter story. Something about its characters just makes me care about them more than those in VLR, too, although I couldn't say what; much as every single character in both games is fantastically well-developed, which I think is one of the reasons I like the games so much, I just care more about each individual in 999. (I do like how they handled the returning ones in VLR, though. Clover might be a bit.. ehh.. compared to how she was before, but I liked that they were able to bring some back without going overboard.)
VLR's gameplay is undoubtedly better, though. What I wouldn't have given to be able to just jump to the appropriate place in 999...
And to be honest, VLR just goes a little bit over the top sometimes. The location, the whole general apocalyptic feel, the fact that
, Dio... Yeah, I think 999. Hella looking forward to ZE3, though.