Where?! Where?! 
It’s an interesting discussion. Personally, with my very amateur involvement with the tools, I’ve found that for me it’s easier to tune voices than instruments.
And, for better or worse, I find that leaving things as they are is sometimes better, IF the performance is self-affirming. There are some notes, sharp ones, that are exactly what should happen, because everything else at this point dictates it. It’s more sentimental than proper. But other times, a pitch might wander up or down unintentionally. These are what I try to correct, but easily sliding the event up or down does not always achieve the purpose. The line of the pitch should also be taken into account, and the nature of the instrument to tune.
Guitar was a great example. Does anyone bother to tune each note? Most are off. Flutes, trumpets, trombones, saxes, everything has its own “blueprint of wrongness”. Each and every note has its quirks. Of course the player strives for good intonation, especially in ensembles, but even then, it’s not a matter of being in the green of the tuner.
Improvements on the side of the algorithm and analysis are welcome, of course. But I agree that the tool is more than good enough for monophonic sources.
(Imagine if we had Polyphonic Variaudio for free in Cubase. A scandal!)