I won't fly on an airline that has crappy service (elderly, burned-out flight attendants) just to get points with the airline alliance I have status with.
For example, given a choice between Cathay Pacific and Air Canada on the same route, I'll choose Cathay every time, even though I do most of my travel with Air Canada and I participate in Air Canada's mileage program.
Paid J is generally the same price on both - but the difference in service, and thus the difference in enjoyment of the flight, is significant.
Similarly, I won't fly on an airline that has crappy lie-flat beds just because it is part of the same alliance as my mileage program... I'll always choose the airline with the best bed, to heck with the points.