I really like Hit Factor scoring with the Minor points scheme. I think that is pretty balanced. I think the criticisms of Hit Factor scoring apply much better to the Major points scheme.
To the questions in the OP, and this is just me talking without giving it a lot of thought, and being pretty exhausted after class all weekend: I think of must-be-clean-or-does-not-count runs of about 7-8 seconds as good, under 7 seconds including penalties under IDPA scoring as good, and under 5 seconds with As/Cs/maybe a D under Hit Factor as good. As for the different ways to score it, I like all of them and just think they end up emphasizing different aspects of shooting.