Sorry, but you're asking for things that clash. By that I mean, the best Shakespeare plays are all well known (and even his lesser plays are pretty well known).
The least known/performed plays are Cymbeline, Timon of Athens, Titus Andronicus, and Pericles (maybe Coriolanus too). If you want the least well-known plays, start looking there.
However, if you want the best male-female scenes, you'll probably have to slide back into the better known plays.
I'm personally very fond of the Titania/Oberon meeting in Act II, scene 1 of A Midsummer Night's Dream. It's well over 150 lines, and is just the two of them (once they are on stage).
If it has to come from one of the lesser known plays and be just a man and a woman, I'd take a peek at Cymbeline, Act III scene 4.
Troilus and Cresida is a goodun. :) Not well known