I would choose to earn ATA points but that's only because I fly both airlines so darn infrequently that I see ATA as a better value - only 3000 points (a single Hawaii trip in Biz or 3 domestic Economy RTs) earns a companion pass for domestic CONUS travel, while 6000 points (just 6 domestic RTs in Economy) earns a free ticket. That's faster than with WN where 8 RTs are needed for a free ticket (excluding promos) and there is no "one-time" companion pass.

Of course, ATA's domestic route structure is more limited so that affects how "valuable" one sees the domestic awards. However, ATA points can also be converted to RR credits, at a rate of 7250 points for 16 RR credits... that means it's STILL only 7.25 domestic RTs for a free ticket, again quicker than WN.

For a frequent flyer who can reach CP level on WN, then WN is probably a better deal. However, for mid-level flyer, it probably all depends on route structures and which airline is most convenient. For the very infrequent flyer (on these airlines) such as myself, I'd say ATA is probably the better value.

(It's also worth noting that frequent ATA flyers can earn elite status, giving them perks including upgrades to Biz on ATA 2-class routes. RR flyers don't have that option if they tend to fly ATA 2-class routes.)