On my wash days I use both a protein leave-in as well as a moisture leave-in. That's the only time I really use "leave-ins." Daily I use a moisture-based moisturizer.
There's not really an answer for your question. It depends on what your hair needs. I hate playing the guessing game so I just mix both kind together and it hasn't failed me yet.
ETA: My response is to the thread title. I don't have a preference, i use both equally.