Sorry, I didn't mean to paint such a bleak picture. There are good and smart people working on these sites, and some newspapers have technically very good code (apart from ads :)
There are also lots of very hard constraints. The publishing process is complex and on strict schedules, especially if it's connected to printing of a daily newspaper. There are hundreds of people involved, so upgrading CMS for a newspaper is like changing wheels of a car while it's moving.
And on top of that monetization on the web is hard. Users hate paywalls. Nobody wants a mobile app, especially not for overpriced in-app payments. But something needs to bring money, and even getting ad inventory that's higher class than "doctors hate this!!!" is also a very hard work.