Interesting issue. To answer your question about the loyalty program, I think we should take a look at the larger airline business world to better understand why Cathay Pacific is not faring as well as it did in the past. In my view, unless Cathay Pacific can figure out a niche strategy they are not going to fare well in the financial skies of tomorrow. This has more to do with market factors:
Several Chinese airlines have expanded their international route systems since they are now able to sufficiently feed their own domestic traffic or can create and sustain standalone specific niche routes between China and both Europe and North America. This directly competes with what seems like Cathay Pacific's feed to Hong Kong and then onward traffic system.
Middle Eastern carriers like Qatar, Emirates, Etihad, and others, have made a much more competitive air travel market.
There are several other considerations but in short, it would, in my view again, be wise to look at Singapore Airlines for long term frequent flyer membership as their business model has really held up well to both Chinese and Middle Eastern competition. Singapore Airlines is also a part of Star Alliance which has some great partners like ANA, Lufthansa, and others.
Hope that helps!