Bill,
I see what you're saying, but what if the two sides are both good, just in different ways? Sure, you could probably parse the question long enough to determine that one is better, but that doesn't necessarily mean the other shouldn't exist.
Take the ninth at Pacific Dunes. I think the upper green probably makes for the better hole of the two, but when the lower is in use it definitely changes your sense of where you'd like to place your tee shot. And I've always liked how those two greens tie in to two different tees on the par-three tenth. JMO, but I think playing to that upper green on #9 (the tougher of the two) makes for an easier tee shot on #10 (though from that spot high in the dunes the shot is more affected by the wind). You can't survey the hole as easily from the lower tee on #10, and while you're shielded from the wind I always have a bit of a harder time with this version of the hole. That's all just my subjective take, but I think it does illustrate the flexibility of Pacific Dunes, the many possibilities the course introduces on a day to day basis... that two-green system on #9 is just one reason why the course is so much fun.