As tablet and phone hardware matures, they should get faster processing power and additional memory that will make these web apps Good Enough (tm). Until that time, like you, I hope the NY Times and others keep making native apps.
Good Flash performance on mobile required both better hardware and efficiently programmed software from Adobe. Adobe is seems to have been a pretty big bottleneck. Flash still works pretty poorly on my desktops and laptops with gobs more power than my phones and tablets.
However, in the case of web apps, we're almost there on performance and we have Google, Apple, Mozilla and Microsoft all working to improve mobile browsers and browser speed.
