Melodic or tonal pitch contour tracking?
I think a PLL would be hard to use for pitch detection in singing or speech. For the reasons you mention (classic phase/frequency comparators output garbage when the waveforms are too different due to a missing f0), but also because you'll need another method anyway for tracking the large changes in pitch or the switch to voice/unvoiced that would put a PLL off the tracks.

A baseline system could be to extract a pitch on small frames with a classic f0 detector (autocorrelation, AMDF, YIN, or any auditory model), and then use dynamic programming (or from another point of view, the Viterbi algorithm on a HMM whose states are discretized pitch values) to recover a pitch track. A ready to use Matlab implementation for this (auditory model + viterbi) is available here or (fancy autocorrelation flavour + dynamic programming) here.

This will be discretized on both the time and pitch axes, but you could then interpolate.