If you are using MIDI Shifting, try adding portamento and/or modeled vibrato. If that doesn't meet your needs, the best solution is to use MIDI correction.

Set your correction window to 600 cents. Prepare to send MIDI notes to your specified MIDIPchCor channel under the MIDI/UTIL menu. Set the attack and amount parameters such that the correction is subtle - retaining your natural pitch fluctuations - but strong enough to alter the pitch of the melody. Now you can play in the re-pitching melody via MIDI and you'll achieve very natural results.